Variant report

Variant	rs4743144
Chromosome Location	chr9:100686120-100686121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:100686046-100686280	LNCaP	prostate:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
2	MYC	chr9:100684236-100686457	K562	blood:	n/a	chr9:100684539-100684548 chr9:100684537-100684550 chr9:100684535-100684550 chr9:100684555-100684564 chr9:100684539-100684548 chr9:100684550-100684569 chr9:100684534-100684553 chr9:100684539-100684549 chr9:100684554-100684565 chr9:100684537-100684550 chr9:100684537-100684550 chr9:100684540-100684549
3	CTCF	chr9:100686120-100686270	HAc	cerebellar:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
4	FOS	chr9:100685488-100686307	MCF10A-Er-Src	breast:	n/a	chr9:100685834-100685843 chr9:100685832-100685843
5	CTCF	chr9:100686100-100686250	SK-N-SH_RA	brain:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
6	CTCF	chr9:100686060-100686210	HPF	lung:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
7	BCLAF1	chr9:100685751-100686416	GM12878	blood:	n/a	n/a
8	CTCF	chr9:100686060-100686210	GM12878	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
9	ZNF143	chr9:100685753-100686358	GM12878	blood:	n/a	n/a
10	RAD21	chr9:100685796-100686357	K562	blood:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936
11	RAD21	chr9:100685645-100686382	HepG2	liver:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936
12	E2F4	chr9:100685603-100686465	MCF10A-Er-Src	breast:	n/a	chr9:100686329-100686338
13	CTCF	chr9:100686100-100686250	HRE	kidney:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
14	RAD21	chr9:100685640-100686601	HCT-116	colon:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936
15	HDAC2	chr9:100686016-100686329	HepG2	liver:	n/a	chr9:100686110-100686119
16	EP300	chr9:100685578-100686290	GM12878	blood:	n/a	chr9:100686054-100686070 chr9:100685833-100685842
17	CTCF	chr9:100686120-100686270	HCT-116	colon:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
18	CTCF	chr9:100686120-100686270	MCF-7	breast:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
19	SIN3AK20	chr9:100685966-100686347	A549	lung:	n/a	n/a
20	ARID3A	chr9:100684260-100686407	HepG2	liver:	n/a	n/a
21	CTCF	chr9:100686080-100686230	AG09319	gingival:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
22	CTCF	chr9:100686000-100686150	MCF-7	breast:	n/a	n/a
23	CTCF	chr9:100686060-100686210	GM12864	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
24	CTCF	chr9:100686080-100686230	Hela-S3	cervix:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
25	CTCF	chr9:100686078-100686253	GM19239	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
26	ATF3	chr9:100685442-100686231	A549	lung:	n/a	n/a
27	CTCF	chr9:100686020-100686170	GM12875	blood:	n/a	n/a
28	CTCF	chr9:100686120-100686270	GM12875	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
29	CTCF	chr9:100686120-100686270	GM12872	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
30	CTCF	chr9:100685503-100686494	K562	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
31	CTCF	chr9:100686100-100686250	HPAF	blood vessel:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
32	CTCF	chr9:100686100-100686250	HCPEpiC	choroid plexus:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
33	CTCF	chr9:100686100-100686250	HFF-Myc	foreskin:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
34	CTCF	chr9:100686060-100686210	AG04450	lung:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
35	CTCF	chr9:100686100-100686250	HBMEC	blood vessel:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
36	STAT1	chr9:100686013-100686174	GM12878	blood:	n/a	n/a
37	RAD21	chr9:100685779-100686440	ECC-1	luminal epithelium:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936
38	HCFC1	chr9:100685998-100686338	K562	blood:	n/a	n/a
39	CTCF	chr9:100685621-100686344	K562	blood:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
40	CTCF	chr9:100685336-100686645	HCT-116	colon:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
41	REST	chr9:100685374-100686153	A549	lung:	n/a	chr9:100685620-100685629 chr9:100686051-100686060
42	CTCF	chr9:100685625-100686411	MCF-7	breast:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
43	CTCF	chr9:100686081-100686235	MCF-7	breast:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
44	CTCF	chr9:100686100-100686250	HMF	breast:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
45	CTCF	chr9:100685812-100686300	Pancreas_OC	pancreas:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100685916-100685934 chr9:100686168-100686184 chr9:100685919-100685932 chr9:100686167-100686185
46	CTCF	chr9:100686060-100686210	AG10803	skin:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
47	CTCF	chr9:100686060-100686210	HFF	foreskin:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
48	CTCF	chr9:100686120-100686270	Hela-S3	cervix:	n/a	chr9:100686172-100686180 chr9:100686170-100686183 chr9:100686169-100686190 chr9:100686168-100686184 chr9:100686167-100686185
49	MAX	chr9:100684143-100686488	A549	lung:	n/a	chr9:100684539-100684548 chr9:100684537-100684550 chr9:100684535-100684550 chr9:100684555-100684564 chr9:100684539-100684548 chr9:100684550-100684569 chr9:100684534-100684553 chr9:100684539-100684549 chr9:100684554-100684565 chr9:100684537-100684550 chr9:100684537-100684550 chr9:100684540-100684549
50	RAD21	chr9:100685590-100686567	MCF-7	breast:	n/a	chr9:100686169-100686183 chr9:100686170-100686177 chr9:100686168-100686187 chr9:100685917-100685936

No.	Distal block	Cell Line	Cell type
1	chr9:100682029..100688801-chr9:100740969..100749393,29	MCF-7	breast:
2	chr9:100685020..100686845-chr9:100716549..100717520,12	K562	blood:
3	chr9:100682922..100687440-chr9:100817123..100820939,8	MCF-7	breast:
4	chr9:100685586..100688165-chr9:100878796..100881297,2	K562	blood:
5	chr9:100685412..100687157-chr9:100698092..100700080,2	MCF-7	breast:
6	chr9:100685930..100687826-chr9:100769901..100771666,3	K562	blood:
7	chr9:100685576..100688537-chr9:100780625..100782385,2	K562	blood:
8	chr9:100684661..100686943-chr9:100794140..100799259,5	K562	blood:
9	chr9:100685710..100686367-chr9:101025985..101026665,3	K562	blood:
10	chr9:100683922..100686421-chr9:100749688..100751954,2	MCF-7	breast:
11	chr9:100393929..100396893-chr9:100683273..100687162,3	K562	blood:
12	chr9:100684640..100686948-chr9:100880759..100882563,2	K562	blood:
13	chr9:100683337..100688322-chr9:101015638..101019207,5	MCF-7	breast:
14	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
15	chr9:100685488..100686354-chr9:100836611..100837303,3	K562	blood:
16	chr9:100683356..100686345-chr9:100832359..100837233,6	MCF-7	breast:
17	chr9:100685383..100686650-chr9:100796663..100797820,11	K562	blood:
18	chr9:100683079..100687048-chr9:101015405..101020638,4	K562	blood:
19	chr9:100685514..100687681-chr9:100731460..100733588,2	K562	blood:
20	chr9:100685632..100686261-chr9:100836444..100836975,2	MCF-7	breast:
21	chr9:100685744..100686543-chr9:100746288..100747162,2	MCF-7	breast:
22	chr9:100682507..100691249-chr9:100739828..100748095,35	MCF-7	breast:
23	chr9:100685658..100686243-chr9:100773528..100774347,2	MCF-7	breast:
24	chr9:100685626..100686321-chr9:100744853..100745599,2	MCF-7	breast:
25	chr9:100685001..100687073-chr9:100804782..100806329,2	K562	blood:
26	chr9:100684278..100686693-chr9:100816052..100820620,8	K562	blood:
27	chr2:131894199..131896837-chr9:100685147..100687682,2	MCF-7	breast:
28	chr9:100685127..100688021-chr9:100778345..100779899,2	MCF-7	breast:
29	chr9:100685705..100686550-chr9:100716442..100717415,9	MCF-7	breast:
30	chr9:100679913..100686278-chr9:100816188..100820459,11	K562	blood:
31	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:
32	chr9:100685785..100686517-chr9:100796418..100797247,3	MCF-7	breast:
33	chr9:100685496..100686599-chr9:101025791..101026677,7	MCF-7	breast:
34	chr9:100683227..100687367-chr9:100758311..100762778,5	K562	blood:
35	chr9:100685498..100686359-chr9:100796718..100798043,9	MCF-7	breast:
36	chr9:100685740..100686377-chr9:100751902..100753253,4	MCF-7	breast:

Variant related genes	Relation type
C9orf156	TF binding region
ENSG00000212521	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000136937	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10512256	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1059003	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10984009	1.00[CEU][hapmap]
rs10984098	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10984377	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10984516	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10984522	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10984532	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10984545	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12156487	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12375612	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12376113	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1348387	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17687621	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1947015	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4514106	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4742708	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743143	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743149	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55978521	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7037172	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7043516	0.88[CEU][hapmap]
rs72753537	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72753557	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72753579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72753581	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72753588	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7851498	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7854948	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100683600-100686400	Active TSS	Thymus	Thymus
2	chr9:100683800-100686200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:100683800-100686200	Active TSS	Fetal Brain Female	brain
4	chr9:100683800-100686200	Active TSS	Rectal Smooth Muscle	rectum
5	chr9:100684000-100686200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:100684000-100686200	Active TSS	Brain Substantia Nigra	brain
7	chr9:100684000-100686200	Active TSS	Fetal Intestine Large	intestine
8	chr9:100684000-100686200	Active TSS	Right Atrium	heart
9	chr9:100684000-100686200	Active TSS	Right Ventricle	heart
10	chr9:100684000-100686400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:100684000-100686400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:100684000-100686400	Active TSS	Brain Angular Gyrus	brain
13	chr9:100684000-100686600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr9:100684000-100687200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:100684200-100686200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:100684200-100686200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:100684200-100686200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:100684400-100686200	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr9:100684600-100686200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:100684600-100686400	Active TSS	Fetal Lung	lung
21	chr9:100684800-100686400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr9:100685000-100686400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr9:100685000-100687000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr9:100685000-100687200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:100685000-100687200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr9:100685200-100687600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:100685400-100686200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr9:100685400-100686200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr9:100685400-100686200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:100685400-100686200	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr9:100685400-100686200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr9:100685400-100686200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr9:100685400-100686200	Enhancers	Fetal Stomach	stomach
34	chr9:100685400-100686200	Enhancers	HSMMtube	muscle
35	chr9:100685400-100686400	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr9:100685400-100686600	Flanking Active TSS	Dnd41	blood
37	chr9:100685400-100687800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr9:100685600-100686200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr9:100685600-100686200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:100685600-100686200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:100685600-100686200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr9:100685600-100686200	Active TSS	Fetal Muscle Leg	muscle
43	chr9:100685600-100686400	Active TSS	Stomach Smooth Muscle	stomach
44	chr9:100685600-100686600	Enhancers	Colon Smooth Muscle	Colon
45	chr9:100685600-100687200	Enhancers	Primary B cells from peripheral blood	blood
46	chr9:100685800-100686200	Active TSS	Primary T cells fromperipheralblood	blood
47	chr9:100685800-100686200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr9:100685800-100686200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:100685800-100686200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:100685800-100686200	Active TSS	Muscle Satellite Cultured Cells	--

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