Variant report

Variant	rs743399
Chromosome Location	chr6:31749804-31749805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31749629-31751091	K562	blood:	n/a	n/a
2	CTCF	chr6:31749800-31749950	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:31749689-31749873	K562	blood:	n/a	n/a
4	ZBTB7A	chr6:31749471-31749856	K562	blood:	n/a	n/a
5	POLR2A	chr6:31747424-31750872	K562	blood:	n/a	n/a
6	POLR2A	chr6:31749086-31750715	HL-60	blood:	n/a	n/a
7	POLR2A	chr6:31749682-31749983	K562	blood:	n/a	n/a
8	POLR2A	chr6:31748512-31750971	K562	blood:	n/a	n/a
9	POLR2A	chr6:31749494-31750580	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:31749345-31750239	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr6:31749522-31750566	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:31743241-31751112	K562	blood:	n/a	n/a
13	POLR2A	chr6:31749294-31750492	GM12892	blood:	n/a	n/a
14	CHD2	chr6:31749637-31749926	K562	blood:	n/a	chr6:31749785-31749795
15	POLR2A	chr6:31747461-31750551	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:31749390-31750584	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:31749499-31749832	GM12892	blood:	n/a	n/a
18	NR2F2	chr6:31749264-31749953	K562	blood:	n/a	n/a
19	POLR2A	chr6:31746625-31750719	K562	blood:	n/a	n/a
20	POLR2A	chr6:31749320-31750801	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr6:31749294-31750636	HepG2	liver:	n/a	n/a
22	POLR2A	chr6:31744267-31750623	SK-N-MC	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31737226..31750413-chr6:31786206..31805473,50	MCF-7	breast:
2	chr6:31747450..31751295-chr6:31800640..31804723,4	MCF-7	breast:
3	chr6:31732922..31735851-chr6:31748037..31750099,2	MCF-7	breast:
4	chr6:31748274..31750464-chr6:31829000..31831442,2	MCF-7	breast:

No data

Variant related genes	Relation type
VARS	TF binding region
ENSG00000201555	TF binding region
VWA7	TF binding region
ENSG00000204387	Chromatin interaction
ENSG00000201754	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000235663	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000204396	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3115673	0.91[ASN][1000 genomes]
rs4711277	0.81[ASN][1000 genomes]
rs480092	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565599	0.93[ASN][1000 genomes]
rs613165	0.86[ASN][1000 genomes]
rs644452	0.86[ASN][1000 genomes]
rs707926	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
10	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
11	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer 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	257 gene(s)	inside rSNPs	diseases
13	nsv884426	chr6:31728102-31800868	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
14	nsv884427	chr6:31728102-31802465	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
15	nsv884428	chr6:31728102-31870326	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
16	nsv884429	chr6:31730356-31837066	Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
17	nsv884430	chr6:31731881-31800631	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
18	nsv884431	chr6:31732679-31761386	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
19	nsv601943	chr6:31733544-31763862	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	55 gene(s)	inside rSNPs	diseases
20	nsv884432	chr6:31734117-31777687	Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
21	nsv884433	chr6:31737701-31777687	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
22	nsv884435	chr6:31739881-31750919	Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases
23	nsv884436	chr6:31739881-31754096	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	35 gene(s)	inside rSNPs	diseases
24	nsv884437	chr6:31739881-31777687	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
25	nsv884438	chr6:31742590-31751832	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic 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	32 gene(s)	inside rSNPs	diseases
26	nsv884439	chr6:31742590-31754096	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	33 gene(s)	inside rSNPs	diseases
27	nsv884440	chr6:31743882-31775984	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
28	nsv884441	chr6:31745518-31754096	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
29	nsv884442	chr6:31745518-31764899	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	43 gene(s)	inside rSNPs	diseases
30	nsv884443	chr6:31745518-31777687	Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
31	nsv601944	chr6:31749541-31763862	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs743399	AIF1	Cis_1M	lymphoblastoid	RTeQTL
rs743399	HSPA1B	Cis_1M	lymphoblastoid	RTeQTL
rs743399	DOM3Z	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31745000-31750600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:31745000-31760200	Weak transcription	Psoas Muscle	Psoas
3	chr6:31745000-31762400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:31745200-31753400	Strong transcription	Brain Germinal Matrix	brain
5	chr6:31745200-31760400	Weak transcription	Fetal Brain Male	brain
6	chr6:31745200-31761000	Strong transcription	Fetal Stomach	stomach
7	chr6:31745400-31751800	Weak transcription	NHDF-Ad	bronchial
8	chr6:31745400-31752000	Strong transcription	Brain Cingulate Gyrus	brain
9	chr6:31745400-31753600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:31745400-31753600	Strong transcription	NHLF	lung
11	chr6:31745400-31753800	Strong transcription	Gastric	stomach
12	chr6:31745400-31755200	Strong transcription	Fetal Brain Female	brain
13	chr6:31745400-31761600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:31745400-31762800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:31745600-31751800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:31745600-31752000	Strong transcription	Brain Hippocampus Middle	brain
17	chr6:31745600-31752000	Strong transcription	Spleen	Spleen
18	chr6:31745600-31752800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:31745600-31753600	Strong transcription	Thymus	Thymus
20	chr6:31745600-31753800	Strong transcription	Esophagus	oesophagus
21	chr6:31745600-31753800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:31745600-31754600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:31745600-31755000	Strong transcription	NHEK	skin
24	chr6:31745600-31755800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:31745600-31758800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:31745600-31759400	Strong transcription	Dnd41	blood
27	chr6:31745600-31760400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:31745600-31760400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:31745600-31760600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:31745600-31760800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:31745600-31760800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:31745600-31760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:31745600-31760800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:31745600-31762200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:31745800-31752200	Strong transcription	Brain Substantia Nigra	brain
36	chr6:31745800-31753600	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr6:31745800-31753600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:31745800-31753600	Strong transcription	Primary T cells from cord blood	blood
39	chr6:31745800-31753600	Strong transcription	Brain Anterior Caudate	brain
40	chr6:31745800-31753600	Strong transcription	Right Ventricle	heart
41	chr6:31745800-31753800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:31745800-31754200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:31745800-31754200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:31745800-31754200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:31745800-31754200	Strong transcription	Fetal Thymus	thymus
46	chr6:31745800-31754600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:31745800-31754600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr6:31745800-31754800	Strong transcription	Placenta	Placenta
49	chr6:31745800-31755000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:31745800-31755400	Strong transcription	H1 Cell Line	embryonic stem cell

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