Variant report

Variant	rs9469860
Chromosome Location	chr6:34724815-34724816
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	USF2	chr6:34724684-34725452	HepG2	liver:	n/a	chr6:34725185-34725201 chr6:34724840-34724851
2	POLR2A	chr6:34724712-34725551	GM18526	blood:	n/a	n/a
3	MAX	chr6:34724679-34725538	HUVEC	blood vessel:	n/a	n/a
4	RUNX3	chr6:34724639-34725611	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:34724594-34725557	ECC-1	luminal epithelium:	n/a	n/a
6	GABPA	chr6:34724742-34725693	SK-N-SH	brain:	n/a	n/a
7	SIN3AK20	chr6:34724648-34725782	MCF-7	breast:	n/a	n/a
8	SIN3AK20	chr6:34724743-34724936	A549	lung:	n/a	n/a
9	EP300	chr6:34724626-34725715	ECC-1	luminal epithelium:	n/a	chr6:34725384-34725400 chr6:34725161-34725175
10	TCF7L2	chr6:34724696-34725592	PANC-1	pancreas:	n/a	chr6:34725153-34725167 chr6:34725152-34725168 chr6:34725548-34725558 chr6:34725152-34725168 chr6:34725152-34725166 chr6:34725545-34725559 chr6:34725155-34725164
11	SP1	chr6:34724687-34725508	HepG2	liver:	n/a	chr6:34725177-34725189 chr6:34725178-34725192 chr6:34725179-34725188 chr6:34725177-34725188 chr6:34725177-34725189 chr6:34725178-34725187 chr6:34725178-34725187 chr6:34725178-34725188 chr6:34725178-34725188
12	MYC	chr6:34724681-34725646	K562	blood:	n/a	n/a
13	POLR2A	chr6:34724751-34725542	NB4	blood:	n/a	n/a
14	MAX	chr6:34724658-34725683	Hela-S3	cervix:	n/a	n/a
15	GATA3	chr6:34724767-34725319	T-47D	breast:	n/a	n/a
16	PAX5	chr6:34724653-34724960	GM12878	blood:	n/a	n/a
17	MXI1	chr6:34724797-34725620	Hela-S3	cervix:	n/a	n/a
18	USF1	chr6:34724638-34725409	A549	lung:	n/a	chr6:34725185-34725201
19	TEAD4	chr6:34724659-34725328	A549	lung:	n/a	n/a
20	POLR2A	chr6:34724653-34724930	HUVEC	blood vessel:	n/a	n/a
21	TAF1	chr6:34724668-34725535	SK-N-SH	brain:	n/a	n/a
22	YY1	chr6:34724714-34725464	SK-N-SH_RA	brain:	n/a	n/a
23	IRF1	chr6:34724770-34725574	K562	blood:	n/a	chr6:34725175-34725189
24	BCL3	chr6:34724717-34725553	A549	lung:	n/a	n/a
25	USF1	chr6:34724598-34725493	SK-N-SH	brain:	n/a	chr6:34725185-34725201
26	POLR2A	chr6:34724566-34725594	PFSK-1	brain:	n/a	n/a
27	CEBPB	chr6:34724647-34725661	GM12878	blood:	n/a	n/a
28	ELK1	chr6:34724781-34725735	K562	blood:	n/a	n/a
29	GABPA	chr6:34724658-34725768	A549	lung:	n/a	n/a
30	TEAD4	chr6:34724642-34725527	ECC-1	luminal epithelium:	n/a	n/a
31	SIN3AK20	chr6:34724750-34725424	A549	lung:	n/a	n/a
32	EP300	chr6:34724747-34725481	HepG2	liver:	n/a	chr6:34725384-34725400 chr6:34725161-34725175
33	POLR2A	chr6:34724684-34725569	GM19099	blood:	n/a	n/a
34	TAF1	chr6:34724614-34725567	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr6:34724729-34725417	A549	lung:	n/a	n/a
36	MAX	chr6:34724607-34725675	A549	lung:	n/a	n/a
37	REST	chr6:34724613-34725884	H1-neurons	neurons:	n/a	chr6:34725183-34725196
38	NFIC	chr6:34724710-34725558	HepG2	liver:	n/a	n/a
39	ATF2	chr6:34724744-34725530	H1-hESC	embryonic stem cell:	n/a	n/a
40	CHD2	chr6:34724789-34725679	K562	blood:	n/a	n/a
41	TEAD4	chr6:34724584-34725572	ECC-1	luminal epithelium:	n/a	n/a
42	USF2	chr6:34724728-34725006	K562	blood:	n/a	chr6:34724840-34724851
43	HEY1	chr6:34724651-34725759	K562	blood:	n/a	n/a
44	CREB1	chr6:34724648-34725770	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr6:34724578-34726123	IMR90	lung:	n/a	n/a
46	SIN3AK20	chr6:34724755-34725635	K562	blood:	n/a	n/a
47	TAF1	chr6:34724651-34725565	PFSK-1	brain:	n/a	n/a
48	MXI1	chr6:34724690-34725621	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:34724735-34725771	PBDE	blood:	n/a	n/a
50	USF1	chr6:34724615-34725524	ECC-1	luminal epithelium:	n/a	chr6:34725185-34725201

No.	Distal block	Cell Line	Cell type
1	chr6:34663247..34666234-chr6:34723415..34727175,3	K562	blood:
2	chr6:34723754..34729214-chr6:34758122..34762652,9	MCF-7	breast:
3	chr21:36260951..36261588-chr6:34724713..34725663,2	Hela-S3	cervix:
4	chr6:34711953..34714210-chr6:34722946..34726652,3	K562	blood:
5	chr6:34723520..34726444-chr6:34854512..34857469,3	MCF-7	breast:
6	chr6:34663247..34666328-chr6:34722695..34726583,8	K562	blood:
7	chr6:34663907..34669185-chr6:34723600..34728462,6	MCF-7	breast:
8	chr6:34392363..34394175-chr6:34723427..34725918,3	MCF-7	breast:
9	chr6:34712695..34714463-chr6:34723596..34725137,2	MCF-7	breast:
10	chr6:34657778..34659720-chr6:34722705..34725050,2	MCF-7	breast:
11	chr6:34658536..34661755-chr6:34723904..34726636,3	MCF-7	breast:
12	chr6:34664585..34666258-chr6:34723626..34725241,2	MCF-7	breast:
13	chr6:34723587..34727193-chr6:34757798..34760917,6	K562	blood:
14	chr6:34723785..34726777-chr6:34759451..34763099,4	MCF-7	breast:

Variant related genes	Relation type
SNRPC	TF binding region
ENSG00000064999	Chromatin interaction
ENSG00000065060	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000217130	Chromatin interaction
ENSG00000272288	Chromatin interaction
ENSG00000159216	Chromatin interaction
ENSG00000124614	Chromatin interaction
ENSG00000238484	Chromatin interaction
ENSG00000196821	Chromatin interaction
ENSG00000270800	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11756392	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759235	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555773	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894959	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883638	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395607	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492859	0.83[EUR][1000 genomes]
rs2744938	0.82[EUR][1000 genomes]
rs2744942	0.83[EUR][1000 genomes]
rs2744947	0.87[EUR][1000 genomes]
rs2744954	0.80[EUR][1000 genomes]
rs2744972	0.87[EUR][1000 genomes]
rs2764203	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764204	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2764205	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	0.82[EUR][1000 genomes]
rs2814948	0.91[EUR][1000 genomes]
rs2814960	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814962	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815005	0.83[EUR][1000 genomes]
rs28567450	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736896	0.90[AFR][1000 genomes]
rs3800457	0.87[EUR][1000 genomes]
rs4472337	0.83[EUR][1000 genomes]
rs56693020	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56930444	0.86[EUR][1000 genomes]
rs59142559	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60643641	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61431557	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457790	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911549	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936177	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6938239	0.94[EUR][1000 genomes]
rs73419607	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73419621	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755822	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762485	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296130	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462012	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9462014	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9462016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462025	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462029	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469864	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469890	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469895	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469897	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469900	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469907	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469910	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469911	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469913	0.85[EUR][1000 genomes]
rs9654581	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688715	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv885795	chr6:34704613-34823187	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv870010	chr6:34713359-34880048	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv1025374	chr6:34723723-34887316	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9469860	C6orf107	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34723600-34725400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:34724000-34725400	Active TSS	Placenta	Placenta
3	chr6:34724000-34725800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:34724200-34725400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:34724200-34725400	Active TSS	Adipose Nuclei	Adipose
6	chr6:34724200-34725400	Active TSS	Liver	Liver
7	chr6:34724200-34725400	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:34724200-34725600	Active TSS	Primary T cells from cord blood	blood
9	chr6:34724200-34725600	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr6:34724200-34725600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr6:34724200-34725600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr6:34724200-34725600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:34724200-34725600	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr6:34724200-34725600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:34724200-34725600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:34724200-34725600	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr6:34724200-34725600	Active TSS	Brain Cingulate Gyrus	brain
18	chr6:34724200-34725600	Active TSS	Colon Smooth Muscle	Colon
19	chr6:34724200-34725600	Active TSS	Duodenum Mucosa	Duodenum
20	chr6:34724200-34725600	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:34724200-34725600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:34724200-34725600	Active TSS	NHEK	skin
23	chr6:34724200-34725800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:34724200-34725800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:34724200-34725800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:34724200-34725800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:34724200-34725800	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr6:34724200-34725800	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:34724200-34725800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:34724200-34725800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:34724200-34725800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:34724200-34725800	Active TSS	Brain Angular Gyrus	brain
33	chr6:34724200-34725800	Active TSS	Brain Anterior Caudate	brain
34	chr6:34724200-34725800	Active TSS	Brain Germinal Matrix	brain
35	chr6:34724200-34725800	Active TSS	Brain Hippocampus Middle	brain
36	chr6:34724200-34725800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr6:34724200-34725800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:34724200-34725800	Active TSS	Brain Substantia Nigra	brain
39	chr6:34724200-34725800	Active TSS	Colonic Mucosa	Colon
40	chr6:34724200-34725800	Active TSS	Esophagus	oesophagus
41	chr6:34724200-34725800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr6:34724200-34725800	Active TSS	Fetal Intestine Large	intestine
43	chr6:34724200-34725800	Active TSS	Fetal Intestine Small	intestine
44	chr6:34724200-34725800	Active TSS	Fetal Lung	lung
45	chr6:34724200-34725800	Active TSS	Fetal Muscle Leg	muscle
46	chr6:34724200-34725800	Active TSS	Fetal Stomach	stomach
47	chr6:34724200-34725800	Active TSS	Fetal Thymus	thymus
48	chr6:34724200-34725800	Active TSS	Left Ventricle	heart
49	chr6:34724200-34725800	Active TSS	Pancreas	Pancrea
50	chr6:34724200-34725800	Active TSS	Rectal Mucosa Donor 29	rectum

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