Variant report

Variant	rs6474736
Chromosome Location	chr9:12818600-12818601
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:12818540-12818690	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr9:12818520-12818670	RPTEC	kidney:	n/a	n/a
3	CTCF	chr9:12818560-12818710	HPF	lung:	n/a	n/a
4	CTCF	chr9:12818560-12818710	HMEC	breast:	n/a	n/a
5	CTCF	chr9:12818561-12818682	A549	lung:	n/a	n/a
6	CTCF	chr9:12818560-12818710	AG09309	skin:	n/a	n/a
7	RAD21	chr9:12818498-12818749	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr9:12818575-12818671	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr9:12818580-12818730	HMF	breast:	n/a	n/a
10	CTCF	chr9:12818540-12818690	AG04450	lung:	n/a	n/a
11	CTCF	chr9:12818552-12818686	MCF-7	breast:	n/a	n/a
12	RAD21	chr9:12818332-12818946	A549	lung:	n/a	n/a
13	CTCF	chr9:12818520-12818670	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr9:12818540-12818690	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr9:12818520-12818670	AG04449	skin:	n/a	n/a
16	CTCF	chr9:12818596-12818647	Pancreas_OC	pancreas:	n/a	n/a
17	CTCF	chr9:12818540-12818690	AG10803	skin:	n/a	n/a
18	CTCF	chr9:12818500-12818650	AG04450	lung:	n/a	n/a
19	CTCF	chr9:12818580-12818730	BE2_C	brain:	n/a	n/a
20	CTCF	chr9:12818500-12818650	NHEK	skin:	n/a	n/a
21	CTCF	chr9:12818520-12818670	HCFaa	heart:	n/a	n/a
22	CTCF	chr9:12818560-12818710	AG10803	skin:	n/a	n/a
23	CTCF	chr9:12818561-12818669	Fibrobl	skin:	n/a	n/a
24	CTCF	chr9:12818600-12818750	HCM	heart:	n/a	n/a
25	GATA3	chr9:12816601-12818747	A549	lung:	n/a	chr9:12816841-12816851 chr9:12816849-12816859
26	CTCF	chr9:12818560-12818710	HCPEpiC	choroid plexus:	n/a	n/a
27	POLR2A	chr9:12818537-12818657	A549	lung:	n/a	n/a
28	CTCF	chr9:12818560-12818710	AG09319	gingival:	n/a	n/a
29	CTCF	chr9:12818493-12818749	IMR90	lung:	n/a	n/a
30	CTCF	chr9:12818500-12818650	SAEC	small airway:	n/a	n/a
31	CTCF	chr9:12818540-12818690	AoAF	blood vessel:	n/a	n/a
32	CTCF	chr9:12818480-12818630	WI-38	lung:	n/a	n/a
33	CTCF	chr9:12818520-12818670	AoAF	blood vessel:	n/a	n/a
34	CTCF	chr9:12818460-12818610	A549	lung:	n/a	n/a
35	CTCF	chr9:12818560-12818710	BE2_C	brain:	n/a	n/a
36	CTCF	chr9:12818540-12818690	GM12864	blood:	n/a	n/a
37	RAD21	chr9:12818438-12818884	A549	lung:	n/a	n/a
38	RAD21	chr9:12818387-12818803	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr9:12818580-12818730	SAEC	small airway:	n/a	n/a
40	RAD21	chr9:12818458-12818782	IMR90	lung:	n/a	n/a
41	CTCF	chr9:12818580-12818730	NHDF-neo	bronchial:	n/a	n/a
42	CTCF	chr9:12818520-12818670	NHLF	lung:	n/a	n/a
43	CTCF	chr9:12818560-12818710	HBMEC	blood vessel:	n/a	n/a
44	RAD21	chr9:12818494-12818783	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr9:12818580-12818730	HEK293	kidney:	n/a	n/a
46	CTCF	chr9:12818520-12818670	HPF	lung:	n/a	n/a
47	CTCF	chr9:12818560-12818710	MCF-7	breast:	n/a	n/a
48	CTCF	chr9:12818580-12818703	ProgFib	skin:	n/a	n/a
49	CTCF	chr9:12818554-12818651	GM10248	blood:	n/a	n/a
50	MAX	chr9:12818497-12818941	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:12810284..12814602-chr9:12816113..12819154,5	MCF-7	breast:
2	chr9:12817203..12820022-chr9:12879979..12881998,2	MCF-7	breast:
3	chr9:12816711..12819917-chr9:12821131..12823680,3	MCF-7	breast:
4	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
5	chr9:12815854..12818984-chr9:12830927..12834079,3	MCF-7	breast:
6	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:
7	chr9:12816957..12819670-chr9:12821766..12823551,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235448	TF binding region
ENSG00000235448	Chromatin interaction
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10960805	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10960806	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10960807	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10960808	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10960810	0.82[CHB][hapmap]
rs10960812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10960813	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6474732	0.90[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6474733	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7846724	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859336	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs957224	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:12814400-12818800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:12814600-12819200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:12814600-12824800	Weak transcription	Psoas Muscle	Psoas
5	chr9:12814800-12823200	Weak transcription	Colonic Mucosa	Colon
6	chr9:12815000-12818800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:12815000-12819200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:12815000-12819800	Enhancers	Fetal Intestine Small	intestine
9	chr9:12815200-12819200	Enhancers	Colon Smooth Muscle	Colon
10	chr9:12815200-12819200	Enhancers	HMEC	breast
11	chr9:12815200-12819600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:12815200-12819800	Enhancers	Fetal Intestine Large	intestine
13	chr9:12815200-12820200	Enhancers	NHLF	lung
14	chr9:12815200-12821400	Enhancers	Osteobl	bone
15	chr9:12815200-12822400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:12815600-12819200	Flanking Active TSS	A549	lung
17	chr9:12815800-12819000	Weak transcription	HUVEC	blood vessel
18	chr9:12815800-12821600	Weak transcription	HSMM	muscle
19	chr9:12816200-12832000	Weak transcription	HSMMtube	muscle
20	chr9:12816600-12819600	Enhancers	Hela-S3	cervix
21	chr9:12816800-12818600	Flanking Active TSS	HepG2	liver
22	chr9:12817000-12819200	Enhancers	Fetal Lung	lung
23	chr9:12817000-12820200	Enhancers	NHDF-Ad	bronchial
24	chr9:12817200-12818600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr9:12817200-12818800	Enhancers	Pancreas	Pancrea
26	chr9:12817200-12819200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:12817200-12819200	Enhancers	Small Intestine	intestine
28	chr9:12817200-12819400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:12817400-12819200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:12817400-12819600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:12817400-12819800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr9:12817600-12818600	Enhancers	Brain Anterior Caudate	brain
33	chr9:12817600-12818800	Enhancers	Brain Cingulate Gyrus	brain
34	chr9:12817600-12819000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:12817600-12819400	Enhancers	Adipose Nuclei	Adipose
36	chr9:12817600-12820000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr9:12817800-12818800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:12817800-12818800	Enhancers	Left Ventricle	heart
39	chr9:12817800-12819200	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:12817800-12819200	Enhancers	Stomach Mucosa	stomach
41	chr9:12817800-12819400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:12817800-12819600	Enhancers	NH-A	brain
43	chr9:12818000-12818600	Weak transcription	Lung	lung
44	chr9:12818000-12819200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr9:12818000-12819200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr9:12818000-12819400	Enhancers	Rectal Smooth Muscle	rectum
47	chr9:12818000-12821200	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:12818000-12821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:12818000-12825000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr9:12818000-12828800	Weak transcription	NHEK	skin

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