Variant report

Variant	rs7756521
Chromosome Location	chr6:30848253-30848254
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	POLR2A	chr6:30848200-30849329	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr6:30848004-30855226	H1-neurons	neurons:	n/a	chr6:30850005-30850018 chr6:30849842-30849855 chr6:30848363-30848383 chr6:30848363-30848383 chr6:30848771-30848781 chr6:30850231-30850245 chr6:30849152-30849172 chr6:30848363-30848383 chr6:30854903-30854911 chr6:30848769-30848782 chr6:30848762-30848775 chr6:30848256-30848264

No.	Distal block	Cell Line	Cell type
1	chr6:30847750..30851239-chr6:30880214..30883075,5	K562	blood:
2	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
3	chr6:30847234..30851507-chr6:30857768..30862295,8	K562	blood:
4	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
5	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
6	chr6:30538571..30540910-chr6:30846758..30849178,2	MCF-7	breast:
7	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
8	chr6:30685105..30690458-chr6:30847596..30854595,13	MCF-7	breast:

Variant related genes	Relation type
DDR1	TF binding region
DDR1-AS1	TF binding region
ENSG00000137331	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000214894	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1049622	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049628	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052693	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947111	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206075	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215246	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215409	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419693	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074508	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074509	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074510	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074511	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2074512	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229933	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239517	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239518	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284175	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284176	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285319	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286655	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524236	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2894055	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213644	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3218802	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218803	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218806	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218814	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218815	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757339	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869085	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869086	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3909130	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41288539	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618569	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711247	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711249	0.82[EUR][1000 genomes]
rs4713402	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457282	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901464	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920760	0.82[EUR][1000 genomes]
rs6921687	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6924600	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743661	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761589	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8408	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916920	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295931	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295932	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295933	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295934	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366761	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368646	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378191	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380200	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380201	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394021	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461638	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468842	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468844	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468845	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468846	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468847	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9501032	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501035	0.82[EUR][1000 genomes]
rs9501342	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv884110	chr6:30845563-30856463	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv884111	chr6:30845563-30864279	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv884112	chr6:30845563-30866618	Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv601482	chr6:30846830-30854090	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884113	chr6:30846830-30857542	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv884114	chr6:30846830-30867830	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv884115	chr6:30847710-30858991	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
14	nsv884116	chr6:30848253-30864279	Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 control	20041166	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7756521	HIST1H2BJ	cis	parietal	SCAN
rs7756521	ZKSCAN4	cis	cerebellum	SCAN
rs7756521	VARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30843600-30848400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30844200-30848600	Enhancers	Fetal Thymus	thymus
3	chr6:30844200-30850200	Weak transcription	Spleen	Spleen
4	chr6:30845400-30848400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:30845400-30848600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:30845600-30848400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:30845600-30848400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:30845600-30848600	Weak transcription	NH-A	brain
9	chr6:30845800-30849800	Weak transcription	Colonic Mucosa	Colon
10	chr6:30845800-30849800	Weak transcription	Right Atrium	heart
11	chr6:30845800-30850000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:30845800-30850800	Weak transcription	Primary T cells from cord blood	blood
13	chr6:30845800-30851200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:30846000-30848400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:30846000-30848400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:30846000-30848400	Weak transcription	Fetal Intestine Small	intestine
17	chr6:30846000-30848400	Weak transcription	HSMMtube	muscle
18	chr6:30846000-30848800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:30846000-30848800	Weak transcription	Brain Angular Gyrus	brain
20	chr6:30846000-30848800	Weak transcription	Fetal Intestine Large	intestine
21	chr6:30846000-30848800	Weak transcription	Placenta	Placenta
22	chr6:30846000-30849000	Weak transcription	Brain Substantia Nigra	brain
23	chr6:30846000-30849000	Weak transcription	HSMM	muscle
24	chr6:30846000-30849200	Weak transcription	HMEC	breast
25	chr6:30846000-30849400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:30846000-30849400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:30846000-30849400	Weak transcription	Thymus	Thymus
28	chr6:30846000-30849400	Weak transcription	NHEK	skin
29	chr6:30846000-30849600	Weak transcription	Pancreas	Pancrea
30	chr6:30846000-30849600	Weak transcription	Stomach Mucosa	stomach
31	chr6:30846000-30849600	Weak transcription	Osteobl	bone
32	chr6:30846000-30849800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:30846000-30849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:30846000-30849800	Weak transcription	NHDF-Ad	bronchial
35	chr6:30846000-30850000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:30846000-30850000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:30846000-30850000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:30846000-30850200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:30846000-30850200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:30846000-30850400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:30846000-30850400	Weak transcription	Left Ventricle	heart
42	chr6:30846000-30850400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:30846000-30850600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:30846000-30850800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr6:30846000-30850800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:30846000-30850800	Weak transcription	Dnd41	blood
47	chr6:30846000-30850800	Enhancers	K562	blood
48	chr6:30846000-30851200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:30846000-30851400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:30846000-30851600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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