Variant report

Variant	rs9379952
Chromosome Location	chr6:26987900-26987901
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:373)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:373 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr6:26987150-26988274	K562	blood:	n/a	n/a
2	NFIC	chr6:26987315-26988431	GM12878	blood:	n/a	n/a
3	MXI1	chr6:26987575-26988341	K562	blood:	n/a	n/a
4	POLR2A	chr6:26987665-26988246	GM12878	blood:	n/a	n/a
5	HDAC2	chr6:26987713-26988098	K562	blood:	n/a	chr6:26988060-26988069
6	E2F6	chr6:26987672-26987939	K562	blood:	n/a	n/a
7	MYC	chr6:26987405-26988339	K562	blood:	n/a	chr6:26987597-26987613
8	EGR1	chr6:26987573-26988238	K562	blood:	n/a	chr6:26987809-26987819 chr6:26987808-26987821
9	MAX	chr6:26987249-26988443	A549	lung:	n/a	chr6:26987597-26987613
10	SP1	chr6:26987806-26988372	A549	lung:	n/a	n/a
11	POLR2A	chr6:26987180-26988394	SK-N-MC	brain:	n/a	n/a
12	TCF7L2	chr6:26987379-26988340	Hela-S3	cervix:	n/a	n/a
13	SRF	chr6:26987824-26988529	ECC-1	luminal epithelium:	n/a	n/a
14	STAT3	chr6:26987440-26988372	MCF10A-Er-Src	breast:	n/a	chr6:26987904-26987915
15	REST	chr6:26987871-26988269	SK-N-SH	brain:	n/a	n/a
16	E2F6	chr6:26987462-26988412	K562	blood:	n/a	chr6:26988021-26988035
17	TCF12	chr6:26987801-26988125	GM12878	blood:	n/a	n/a
18	BHLHE40	chr6:26987590-26988182	GM12878	blood:	n/a	n/a
19	YY1	chr6:26987857-26988284	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:26987750-26988223	GM12891	blood:	n/a	n/a
21	TCF7L2	chr6:26987558-26988214	MCF-7	breast:	n/a	n/a
22	SP1	chr6:26987698-26988221	GM12878	blood:	n/a	n/a
23	SIN3AK20	chr6:26987550-26987952	H1-hESC	embryonic stem cell:	n/a	n/a
24	IRF1	chr6:26987757-26988376	K562	blood:	n/a	chr6:26987897-26987917 chr6:26987903-26987914 chr6:26987901-26987915 chr6:26987895-26987912 chr6:26987901-26987918 chr6:26987899-26987916 chr6:26987903-26987916 chr6:26987898-26987911 chr6:26987902-26987916
25	TAF1	chr6:26987439-26988281	A549	lung:	n/a	n/a
26	MAX	chr6:26987382-26988391	H1-hESC	embryonic stem cell:	n/a	chr6:26987597-26987613
27	TAF1	chr6:26987791-26988274	GM12878	blood:	n/a	n/a
28	POU2F2	chr6:26987825-26988238	GM12878	blood:	n/a	n/a
29	RUNX3	chr6:26987410-26988413	GM12878	blood:	n/a	n/a
30	SREBP2	chr6:26987716-26989036	GM12878	blood:	n/a	n/a
31	ZNF143	chr6:26987752-26988419	K562	blood:	n/a	n/a
32	POLR2A	chr6:26986701-26988296	MCF10A-Er-Src	breast:	n/a	n/a
33	TAF1	chr6:26987286-26988416	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP1	chr6:26987425-26988489	A549	lung:	n/a	n/a
35	PAX5	chr6:26987767-26988229	GM12878	blood:	n/a	n/a
36	NFATC1	chr6:26987537-26988492	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:26987172-26988332	Hela-S3	cervix:	n/a	n/a
38	ATF1	chr6:26987625-26988307	K562	blood:	n/a	n/a
39	GABPA	chr6:26987855-26988272	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:26987837-26988134	GM18951	blood:	n/a	n/a
41	GABPA	chr6:26987845-26988299	H1-hESC	embryonic stem cell:	n/a	n/a
42	GABPA	chr6:26987393-26988560	SK-N-SH	brain:	n/a	n/a
43	EGR1	chr6:26987584-26988209	H1-hESC	embryonic stem cell:	n/a	chr6:26987809-26987819 chr6:26987808-26987821
44	GABPA	chr6:26987342-26988459	SK-N-SH	brain:	n/a	n/a
45	SRF	chr6:26987664-26988470	MCF-7	breast:	n/a	n/a
46	POLR2A	chr6:26987370-26988239	SK-N-MC	brain:	n/a	n/a
47	SRF	chr6:26987868-26988305	H1-hESC	embryonic stem cell:	n/a	n/a
48	FOXA2	chr6:26987505-26988326	A549	lung:	n/a	n/a
49	TCF7L2	chr6:26987479-26988219	PANC-1	pancreas:	n/a	n/a
50	YY1	chr6:26987810-26988324	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26986672..26989789-chr6:27000178..27003902,5	K562	blood:
2	chr6:26987473..26989344-chr6:26998770..27002540,3	MCF-7	breast:
3	chr17:57784521..57785212-chr6:26987452..26988274,2	Hela-S3	cervix:
4	chr6:26985450..26988105-chr6:27045850..27047500,2	MCF-7	breast:
5	chr6:26986141..26989315-chr6:27099693..27102722,3	K562	blood:
6	chr6:26596362..26598030-chr6:26986586..26989465,2	MCF-7	breast:
7	chr19:14628712..14629433-chr6:26987153..26987946,2	Hela-S3	cervix:
8	chr6:26986048..26988342-chr8:145752952..145755516,2	MCF-7	breast:
9	chr17:41465565..41466625-chr6:26987146..26987924,3	Hela-S3	cervix:
10	chr6:26923074..26925467-chr6:26986570..26988926,2	K562	blood:
11	chr17:41438167..41438688-chr6:26987450..26987968,2	Hela-S3	cervix:
12	chr6:26987456..26989789-chr6:27000178..27002693,2	K562	blood:
13	chr6:26595477..26598975-chr6:26986599..26989051,3	K562	blood:
14	chr6:26987415..26988064-chr6:28891401..28892216,2	Hela-S3	cervix:
15	chr6:26985479..26987950-chr6:27115470..27119189,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2BJ-8	chr6:26987145-26988085	NONHSAT108323
2	lnc-HIST1H2BJ-8	chr6:26985858-26989416	NONHSAT108322

No data

Variant related genes	Relation type
LINC00240	TF binding region
TRNAI2	TF binding region
ENSG00000188825	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000220581	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000241549	Chromatin interaction
ENSG00000224843	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000213563	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000141378	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10456350	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10498732	0.87[EUR][1000 genomes]
rs10946881	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs10946882	0.84[EUR][1000 genomes]
rs12191522	0.83[EUR][1000 genomes]
rs12202233	0.84[EUR][1000 genomes]
rs12203587	0.87[EUR][1000 genomes]
rs12203782	1.00[CEU][hapmap]
rs12206880	0.81[EUR][1000 genomes]
rs12661756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2038538	0.82[EUR][1000 genomes]
rs2754603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3931463	0.87[EUR][1000 genomes]
rs3931464	0.87[EUR][1000 genomes]
rs3999248	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4358615	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4440454	0.97[ASN][1000 genomes]
rs4634448	0.81[EUR][1000 genomes]
rs62402024	0.85[EUR][1000 genomes]
rs62402025	0.86[EUR][1000 genomes]
rs6905284	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6907403	0.80[CHB][hapmap]
rs6918835	0.92[EUR][1000 genomes]
rs6930959	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71559004	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755054	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7775041	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9348742	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348743	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs9348746	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9357030	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366679	0.99[ASN][1000 genomes]
rs9368480	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368481	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9368483	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368484	0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368485	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9368488	0.87[JPT][hapmap]
rs9379949	0.96[ASN][1000 genomes]
rs9379950	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379957	0.81[JPT][hapmap]
rs9393786	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
5	nsv469610	chr6:26841083-26999230	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv482509	chr6:26841083-26999230	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv471636	chr6:26841084-27038175	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv469675	chr6:26848950-27015598	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv482429	chr6:26848950-27015598	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv830616	chr6:26859097-27030476	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	esv1810582	chr6:26889428-26990246	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv469625	chr6:26893739-27038175	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv482537	chr6:26893739-27038175	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	esv15177	chr6:26916403-26987915	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9379952	RP11-457M11.5	cis	Adipose Subcutaneous	GTEx
rs9379952	RP11-457M11.5	cis	Muscle Skeletal	GTEx
rs9379952	RP11-457M11.5	cis	lung	GTEx
rs9379952	RP11-457M11.5	cis	Nerve Tibial	GTEx
rs9379952	RP11-457M11.5	cis	Artery Tibial	GTEx
rs9379952	RP11-457M11.5	cis	Whole Blood	GTEx
rs9379952	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs9379952	RP11-457M11.5	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26986200-26988600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:26986200-26988600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:26986200-26988800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:26986400-26988400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:26986400-26988600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:26986400-26988800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:26986400-26988800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:26986600-26988200	Active TSS	Hela-S3	cervix
9	chr6:26986600-26988400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr6:26986600-26988600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:26986600-26988600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:26986600-26988600	Active TSS	Brain Cingulate Gyrus	brain
13	chr6:26986600-26988600	Active TSS	Brain Hippocampus Middle	brain
14	chr6:26986600-26988600	Active TSS	Fetal Brain Female	brain
15	chr6:26986600-26988600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:26986600-26988600	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr6:26986600-26988600	Active TSS	Stomach Smooth Muscle	stomach
18	chr6:26986800-26988200	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr6:26986800-26988200	Active TSS	Fetal Lung	lung
20	chr6:26986800-26988200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr6:26986800-26988400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:26986800-26988400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:26986800-26988400	Active TSS	Fetal Heart	heart
24	chr6:26986800-26988400	Active TSS	Psoas Muscle	Psoas
25	chr6:26986800-26988400	Active TSS	NHLF	lung
26	chr6:26986800-26988600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr6:26986800-26988600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:26986800-26988600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:26986800-26988600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:26986800-26988600	Active TSS	Brain Angular Gyrus	brain
31	chr6:26986800-26988600	Active TSS	Brain Anterior Caudate	brain
32	chr6:26986800-26988600	Active TSS	Fetal Intestine Large	intestine
33	chr6:26986800-26988600	Active TSS	Rectal Smooth Muscle	rectum
34	chr6:26986800-26988600	Active TSS	Right Ventricle	heart
35	chr6:26986800-26988600	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr6:26986800-26988600	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr6:26986800-26988600	Active TSS	NHDF-Ad	bronchial
38	chr6:26986800-26988800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:26986800-26988800	Active TSS	Duodenum Mucosa	Duodenum
40	chr6:26987000-26988200	Active TSS	Fetal Intestine Small	intestine
41	chr6:26987000-26988200	Active TSS	K562	blood
42	chr6:26987000-26988400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:26987000-26988400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr6:26987000-26988400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:26987000-26988400	Active TSS	Ovary	ovary
46	chr6:26987000-26988400	Active TSS	Placenta Amnion	Placenta Amnion
47	chr6:26987000-26988400	Active TSS	A549	lung
48	chr6:26987000-26988600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:26987000-26988600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:26987000-26988600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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