Variant report

Variant	rs4614910
Chromosome Location	chr2:10829416-10829417
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr2:10829291-10830344	HepG2	liver:	n/a	n/a
2	MAX	chr2:10829253-10830313	K562	blood:	n/a	n/a
3	POLR2A	chr2:10829271-10830756	GM12891	blood:	n/a	n/a
4	MAZ	chr2:10829385-10830349	IMR90	lung:	n/a	n/a
5	MXI1	chr2:10829285-10830292	K562	blood:	n/a	n/a
6	MAX	chr2:10829416-10830319	SK-N-SH	brain:	n/a	n/a
7	RCOR1	chr2:10829261-10829722	K562	blood:	n/a	n/a
8	POLR2A	chr2:10829087-10830782	HepG2	liver:	n/a	n/a
9	MXI1	chr2:10829370-10830349	GM12878	blood:	n/a	n/a
10	MYC	chr2:10829364-10830352	K562	blood:	n/a	n/a
11	MTA3	chr2:10829280-10830687	GM12878	blood:	n/a	n/a
12	SIN3A	chr2:10829213-10830659	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:10829282-10831867	MCF10A-Er-Src	breast:	n/a	n/a
14	HCFC1	chr2:10829365-10830415	Hela-S3	cervix:	n/a	n/a
15	MAX	chr2:10829327-10830446	HepG2	liver:	n/a	n/a
16	MAX	chr2:10829329-10830418	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:10829410-10830509	HUVEC	blood vessel:	n/a	n/a
18	SIN3AK20	chr2:10829317-10830313	K562	blood:	n/a	n/a
19	POLR2A	chr2:10828949-10829574	GM12878	blood:	n/a	n/a
20	MAX	chr2:10829381-10830324	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3AK20	chr2:10829389-10830382	MCF-7	breast:	n/a	n/a
22	MXI1	chr2:10828475-10830867	SK-N-SH	brain:	n/a	n/a
23	MAX	chr2:10829395-10830306	SK-N-SH	brain:	n/a	n/a
24	SIN3A	chr2:10829371-10830386	GM12878	blood:	n/a	n/a
25	BCL3	chr2:10829102-10830373	A549	lung:	n/a	n/a
26	MYC	chr2:10829254-10829749	MCF10A-Er-Src	breast:	n/a	n/a
27	SIN3AK20	chr2:10829290-10830798	SK-N-SH	brain:	n/a	n/a
28	GABPA	chr2:10829173-10830603	MCF-7	breast:	n/a	n/a
29	TEAD4	chr2:10829276-10830340	HepG2	liver:	n/a	n/a
30	MBD4	chr2:10829298-10830368	HepG2	liver:	n/a	n/a
31	SIN3AK20	chr2:10829276-10830422	MCF-7	breast:	n/a	n/a
32	MAX	chr2:10829404-10830338	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr2:10829216-10829754	A549	lung:	n/a	n/a
34	MAX	chr2:10829279-10830879	HCT-116	colon:	n/a	n/a
35	MAX	chr2:10829335-10830872	HCT-116	colon:	n/a	n/a
36	MYC	chr2:10829386-10830502	A549	lung:	n/a	n/a
37	MYC	chr2:10829408-10830358	NB4	blood:	n/a	n/a
38	WRNIP1	chr2:10829152-10830261	GM12878	blood:	n/a	n/a
39	SIN3AK20	chr2:10829376-10830288	K562	blood:	n/a	n/a
40	MAX	chr2:10829413-10830295	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr2:10829261-10830435	PBDE	blood:	n/a	n/a
42	TCF12	chr2:10829378-10830831	A549	lung:	n/a	n/a
43	MAX	chr2:10829362-10830465	MCF-7	breast:	n/a	n/a
44	JUN	chr2:10828996-10830489	K562	blood:	n/a	n/a
45	IRF1	chr2:10829379-10830356	K562	blood:	n/a	n/a
46	MYC	chr2:10829393-10830418	K562	blood:	n/a	n/a
47	GABPA	chr2:10829368-10830786	A549	lung:	n/a	n/a
48	MXI1	chr2:10828882-10830424	IMR90	lung:	n/a	n/a
49	MAX	chr2:10829307-10830421	ECC-1	luminal epithelium:	n/a	n/a
50	CREB1	chr2:10829256-10830427	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10804991..10808517-chr2:10827670..10830075,3	K562	blood:
2	chr2:10828248..10829978-chr2:10860553..10862190,2	MCF-7	breast:
3	chr2:10828658..10831241-chr2:10859513..10862984,4	MCF-7	breast:
4	chr2:10584788..10589777-chr2:10826863..10830293,6	K562	blood:
5	chr2:10828291..10832221-chr2:11269738..11273006,3	MCF-7	breast:
6	chr2:10829183..10831676-chr2:10953297..10956112,2	MCF-7	breast:

No data

Variant related genes	Relation type
RN7SL832P	TF binding region
ENSG00000206633	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000238962	Chromatin interaction
ENSG00000143882	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000257135	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10178212	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195255	0.80[CHD][hapmap]
rs11695330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586622	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1586623	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17364547	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17364568	0.90[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2110775	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2357656	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233884	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233885	0.83[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4586606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669605	0.81[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4669606	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669607	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58445061	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72777324	0.89[ASN][1000 genomes]
rs72777332	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72777335	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7572631	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs7593172	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759398	0.90[CEU][hapmap];0.89[JPT][hapmap]
rs881572	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4614910	CYS1	cis	cerebellum	SCAN
rs4614910	PDIA6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10828200-10829600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:10828200-10829800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:10828200-10829800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:10828200-10829800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr2:10828200-10831200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:10828600-10829600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr2:10828600-10829800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr2:10828600-10829800	Flanking Active TSS	Osteobl	bone
9	chr2:10828600-10830000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr2:10828600-10830600	Active TSS	Pancreas	Pancrea
11	chr2:10828600-10830800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:10828800-10829600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr2:10828800-10829600	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr2:10828800-10829600	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr2:10828800-10829600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:10828800-10829600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr2:10828800-10829600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr2:10828800-10829600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:10828800-10829600	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr2:10828800-10829600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:10828800-10829600	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr2:10828800-10829600	Flanking Active TSS	Thymus	Thymus
23	chr2:10828800-10829600	Flanking Active TSS	HUVEC	blood vessel
24	chr2:10828800-10829800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:10828800-10829800	Flanking Active TSS	Liver	Liver
26	chr2:10828800-10829800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr2:10828800-10831000	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr2:10829000-10829600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr2:10829000-10829600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:10829000-10829600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:10829000-10829600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:10829000-10829600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:10829000-10829600	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr2:10829000-10829600	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr2:10829000-10829600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:10829000-10829600	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr2:10829000-10829600	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr2:10829000-10829600	Flanking Active TSS	Fetal Brain Male	brain
39	chr2:10829000-10829600	Flanking Active TSS	Fetal Heart	heart
40	chr2:10829000-10829600	Flanking Active TSS	Fetal Kidney	kidney
41	chr2:10829000-10829600	Flanking Active TSS	Fetal Lung	lung
42	chr2:10829000-10829600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:10829000-10829800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr2:10829000-10829800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr2:10829000-10829800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr2:10829000-10829800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr2:10829000-10829800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr2:10829000-10829800	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr2:10829000-10829800	Flanking Active TSS	Fetal Thymus	thymus
50	chr2:10829000-10830000	Flanking Active TSS	Primary B cells from cord blood	blood

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