Variant report

Variant	rs2684941
Chromosome Location	chr15:34331782-34331783
allele	A/G
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	chr15:34330481-34332349	GM18505	blood:	n/a	n/a
2	USF1	chr15:34331692-34331924	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr15:34330251-34332230	A549	lung:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34330945-34330952 chr15:34331839-34331848 chr15:34331838-34331849
4	POLR2A	chr15:34330445-34332311	GM19099	blood:	n/a	n/a
5	MYC	chr15:34330125-34332263	NB4	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34330945-34330952 chr15:34331839-34331848 chr15:34331838-34331849
6	MYC	chr15:34331773-34331862	HepG2	liver:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
7	POLR2A	chr15:34330437-34332751	GM12878	blood:	n/a	n/a
8	MAX	chr15:34330280-34332085	A549	lung:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34330945-34330952 chr15:34331839-34331848 chr15:34331838-34331849
9	MAX	chr15:34331682-34332166	GM12878	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
10	POLR2A	chr15:34330277-34332169	NB4	blood:	n/a	n/a
11	MYC	chr15:34330048-34332010	MCF10A-Er-Src	breast:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34330945-34330952 chr15:34331839-34331848 chr15:34331838-34331849
12	POLR2A	chr15:34330472-34332118	GM12892	blood:	n/a	n/a
13	POLR2A	chr15:34331674-34332188	GM12891	blood:	n/a	n/a
14	MAX	chr15:34330425-34332206	GM12878	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34330945-34330952 chr15:34331839-34331848 chr15:34331838-34331849
15	POLR2A	chr15:34330319-34332548	GM12891	blood:	n/a	n/a
16	E2F6	chr15:34330370-34332027	K562	blood:	n/a	chr15:34331345-34331352 chr15:34331883-34331894 chr15:34331458-34331470 chr15:34330606-34330615
17	MTA3	chr15:34331635-34332288	GM12878	blood:	n/a	n/a
18	MYC	chr15:34331649-34332221	MCF10A-Er-Src	breast:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
19	POLR2A	chr15:34330228-34332241	Raji	blood:	n/a	n/a
20	USF1	chr15:34331617-34331999	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr15:34331638-34332185	GM12892	blood:	n/a	n/a
22	POLR2A	chr15:34331681-34331963	GM12891	blood:	n/a	n/a
23	MAX	chr15:34331748-34331984	K562	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
24	STAT3	chr15:34331636-34332260	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:34330415-34332413	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:34331550-34332223	GM12892	blood:	n/a	n/a
27	MAX	chr15:34331679-34332040	H1-hESC	embryonic stem cell:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
28	STAT1	chr15:34331776-34332131	GM12878	blood:	n/a	n/a
29	MAX	chr15:34330316-34332273	NB4	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34330945-34330952 chr15:34331839-34331848 chr15:34331838-34331849
30	MAX	chr15:34331710-34332061	SK-N-SH	brain:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
31	RUNX3	chr15:34331627-34332281	GM12878	blood:	n/a	n/a
32	MAX	chr15:34331666-34332064	HepG2	liver:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
33	POLR2A	chr15:34331701-34332240	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:34330018-34332279	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr15:34330300-34332253	GM12892	blood:	n/a	n/a
36	BRCA1	chr15:34331653-34332077	Hela-S3	cervix:	n/a	n/a
37	CREB1	chr15:34331663-34332209	GM12878	blood:	n/a	n/a
38	MXI1	chr15:34330393-34332205	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:34331729-34331953	GM12878	blood:	n/a	n/a
40	MAX	chr15:34331634-34332036	H1-hESC	embryonic stem cell:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
41	MAX	chr15:34331724-34332078	K562	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
42	RUNX3	chr15:34331614-34332299	GM12878	blood:	n/a	n/a
43	BHLHE40	chr15:34331683-34332316	GM12878	blood:	n/a	n/a
44	MAX	chr15:34331750-34332070	H1-hESC	embryonic stem cell:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
45	MAX	chr15:34331734-34331959	K562	blood:	n/a	chr15:34331840-34331847 chr15:34331838-34331849 chr15:34331839-34331848 chr15:34331838-34331849
46	USF2	chr15:34331700-34332075	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:34330080-34333046	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr15:34330512-34332125	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:34331629-34332104	GM12892	blood:	n/a	n/a
50	BATF	chr15:34331690-34332086	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:34330030..34332710-chr15:35259474..35262090,2	MCF-7	breast:
2	chr15:34329770..34332450-chr15:34500868..34502911,3	K562	blood:
3	chr15:34330950..34333091-chr15:34501411..34503652,2	K562	blood:

Variant related genes	Relation type
AVEN	TF binding region
ENSG00000134152	Chromatin interaction
ENSG00000021776	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12902762	0.81[ASN][1000 genomes]
rs1872806	0.85[ASN][1000 genomes]
rs2078561	0.84[ASN][1000 genomes]
rs2078562	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2243858	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2632075	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2632076	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs2632078	0.85[ASN][1000 genomes]
rs2632079	0.85[ASN][1000 genomes]
rs2632107	0.85[ASN][1000 genomes]
rs2684931	0.92[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2684932	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2684939	0.93[ASN][1000 genomes]
rs2684943	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2684956	0.81[ASN][1000 genomes]
rs2702278	0.83[ASN][1000 genomes]
rs2702281	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2702282	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2702284	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2702285	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2702306	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28432827	0.80[ASN][1000 genomes]
rs28667556	0.81[ASN][1000 genomes]
rs3794592	0.80[ASN][1000 genomes]
rs3861194	0.82[ASN][1000 genomes]
rs481391	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5016373	0.87[ASN][1000 genomes]
rs522397	0.88[CEU][hapmap]
rs543621	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55805034	0.86[ASN][1000 genomes]
rs613479	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs623941	0.88[CEU][hapmap]
rs625596	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6495459	0.83[CHB][hapmap]
rs682052	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030334	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs8040776	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs893138	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong 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	18 gene(s)	inside rSNPs	diseases
5	esv3368275	chr15:34330085-34332358	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2684941	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34330000-34331800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:34330000-34331800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr15:34330000-34331800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:34330000-34331800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:34330000-34331800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:34330000-34331800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr15:34330000-34331800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:34330000-34331800	Active TSS	Brain Cingulate Gyrus	brain
9	chr15:34330000-34331800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr15:34330000-34331800	Active TSS	Brain Substantia Nigra	brain
11	chr15:34330000-34331800	Active TSS	Fetal Brain Female	brain
12	chr15:34330000-34331800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr15:34330000-34331800	Active TSS	Thymus	Thymus
14	chr15:34330000-34332000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:34330000-34332000	Active TSS	Colonic Mucosa	Colon
16	chr15:34330000-34332000	Active TSS	Fetal Muscle Leg	muscle
17	chr15:34330000-34332000	Active TSS	Psoas Muscle	Psoas
18	chr15:34330000-34332000	Active TSS	Right Ventricle	heart
19	chr15:34330000-34332200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:34330000-34332200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:34330000-34332200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr15:34330000-34332400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:34330200-34331800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:34330200-34331800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:34330200-34331800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:34330200-34331800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:34330200-34331800	Active TSS	Brain Anterior Caudate	brain
28	chr15:34330200-34331800	Active TSS	Fetal Intestine Small	intestine
29	chr15:34330200-34331800	Active TSS	Ovary	ovary
30	chr15:34330200-34331800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr15:34330200-34331800	Active TSS	Stomach Smooth Muscle	stomach
32	chr15:34330200-34331800	Active TSS	HSMM	muscle
33	chr15:34330200-34332000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:34330200-34332000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:34330200-34332000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:34330200-34332000	Active TSS	Fetal Muscle Trunk	muscle
37	chr15:34330400-34331800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:34330400-34331800	Active TSS	Brain Angular Gyrus	brain
39	chr15:34330400-34331800	Active TSS	Brain Hippocampus Middle	brain
40	chr15:34330400-34331800	Active TSS	Left Ventricle	heart
41	chr15:34330400-34331800	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr15:34330400-34331800	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr15:34330400-34332000	Active TSS	Fetal Stomach	stomach
44	chr15:34330600-34331800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:34330600-34331800	Active TSS	Primary T cells from cord blood	blood
46	chr15:34330600-34331800	Active TSS	Duodenum Mucosa	Duodenum
47	chr15:34330600-34331800	Active TSS	HSMMtube	muscle
48	chr15:34330600-34331800	Active TSS	NHLF	lung
49	chr15:34330800-34331800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:34331000-34332200	Active TSS	Aorta	Aorta

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