Variant report

Variant	rs6965250
Chromosome Location	chr7:12770454-12770455
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:12768354..12771175-chr7:12788288..12790278,2	K562	blood:
2	chr7:12725861..12727450-chr7:12769248..12771413,2	K562	blood:
3	chr7:12758686..12761264-chr7:12769370..12772291,2	MCF-7	breast:
4	chr7:12769733..12771692-chr8:55206827..55208347,2	K562	blood:
5	chr7:12769404..12771505-chr7:12844117..12845724,2	K562	blood:
6	chr7:12443181..12445165-chr7:12769138..12771677,2	K562	blood:
7	chr7:12729128..12735523-chr7:12765929..12775781,12	K562	blood:
8	chr7:12768764..12771206-chr7:12785480..12787516,3	K562	blood:
9	chr7:12762443..12764537-chr7:12768925..12771738,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000146530	Chromatin interaction
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10227444	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10228478	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10228692	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10229334	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10230505	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10232476	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10232482	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10232492	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10233392	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10241274	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10251149	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10251270	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10253749	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10266373	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10271036	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11973922	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11973968	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11980726	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11980770	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11981654	1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11984319	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11984405	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13242844	0.92[EUR][1000 genomes]
rs1357820	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1357821	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1404521	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1524936	1.00[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1830019	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1917489	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1917490	0.91[EUR][1000 genomes]
rs2058046	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2108471	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2140745	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2204398	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2884002	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34478352	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34687763	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34903132	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35983470	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4428564	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4721128	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4721129	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4721130	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4721131	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4721132	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4721133	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55864612	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55899328	0.89[EUR][1000 genomes]
rs56309306	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57452384	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59470504	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6460975	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6460976	1.00[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6949193	1.00[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6954600	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6955313	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6956267	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6961147	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6965183	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6965370	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6971540	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6973261	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6977767	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6978369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978451	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6979212	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7787729	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7789825	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7789972	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7790314	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7790399	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7792091	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs7792774	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802097	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7806690	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9690109	0.87[EUR][1000 genomes]
rs9690689	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9690691	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9691242	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9692011	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs976215	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	esv2422346	chr7:12739291-12883550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1027501	chr7:12743592-12927109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv887641	chr7:12747443-12782062	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
10	esv3336848	chr7:12770395-12770622	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6965250	ARL4A	cis	multi-tissue	Pritchard
rs6965250	VWDE	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12756400-12770800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:12756600-12770800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:12758000-12770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:12759200-12771200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:12760400-12770600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:12760400-12770800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:12762600-12770800	Weak transcription	Stomach Mucosa	stomach
8	chr7:12762800-12770800	Weak transcription	Small Intestine	intestine
9	chr7:12766600-12771800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:12766600-12772000	Enhancers	HUVEC	blood vessel
11	chr7:12766800-12771600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr7:12767800-12770800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:12767800-12771200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:12768000-12771600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:12768400-12770800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:12768400-12771000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:12768600-12771800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr7:12768800-12771600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr7:12769000-12771800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:12769200-12770600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:12769200-12770600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:12769200-12770600	Weak transcription	Hela-S3	cervix
23	chr7:12769200-12770600	Weak transcription	HMEC	breast
24	chr7:12769200-12770600	Weak transcription	NHEK	skin
25	chr7:12769200-12770800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:12769200-12770800	Weak transcription	Brain Angular Gyrus	brain
27	chr7:12769200-12770800	Weak transcription	Esophagus	oesophagus
28	chr7:12769200-12770800	Weak transcription	Left Ventricle	heart
29	chr7:12769200-12770800	Weak transcription	Right Atrium	heart
30	chr7:12769200-12770800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:12769200-12771000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:12769200-12771200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:12769200-12771600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:12769400-12772400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:12769600-12771600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:12769600-12772400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:12769800-12770600	Weak transcription	Psoas Muscle	Psoas
38	chr7:12769800-12770800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:12769800-12770800	Weak transcription	Ovary	ovary
40	chr7:12769800-12771800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr7:12769800-12772200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr7:12770000-12771200	Enhancers	Fetal Stomach	stomach
43	chr7:12770000-12771600	Enhancers	A549	lung
44	chr7:12770000-12771800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:12770000-12772000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr7:12770000-12772000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr7:12770000-12772400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr7:12770200-12770800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr7:12770200-12771400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:12770200-12771400	Enhancers	HUES6 Cell Line	embryonic stem cell

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