Variant report

Variant	rs6944865
Chromosome Location	chr7:4766383-4766384
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	chr7:4750973..4755247-chr7:4763506..4767347,8	MCF-7	breast:
2	chr7:4721561..4725553-chr7:4763080..4767294,4	MCF-7	breast:
3	chr7:4720287..4723602-chr7:4763123..4767792,8	MCF-7	breast:
4	chr7:4762980..4766999-chr7:4782747..4785912,5	MCF-7	breast:
5	chr7:4759871..4762762-chr7:4764322..4767254,4	MCF-7	breast:
6	chr7:4680335..4683615-chr7:4763536..4766738,3	MCF-7	breast:
7	chr7:4680348..4683879-chr7:4764377..4769101,7	MCF-7	breast:
8	chr7:4765455..4768723-chr7:4771595..4773109,3	MCF-7	breast:
9	chr7:4760150..4762017-chr7:4764864..4767459,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164916	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10228886	0.89[CEU][hapmap];0.84[GIH][hapmap]
rs10232008	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10261971	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11765781	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs12701913	0.89[EUR][1000 genomes]
rs13228233	0.86[JPT][hapmap]
rs3087749	0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4077986	1.00[ASN][1000 genomes]
rs4492258	0.97[ASN][1000 genomes]
rs4523152	0.86[JPT][hapmap]
rs4540325	0.86[JPT][hapmap]
rs4720401	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4720402	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4724033	1.00[JPT][hapmap]
rs6946034	1.00[ASN][1000 genomes]
rs6950090	1.00[ASN][1000 genomes]
rs6973046	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7781456	1.00[JPT][hapmap]
rs7793919	0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]

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	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv508442	chr7:4623264-4769628	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6944865	FOXK1	cis	Whole Blood	GTEx
rs6944865	RAC1	cis	parietal	SCAN
rs6944865	ZNF12	cis	parietal	SCAN
rs6944865	PMS2CL	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4753400-4774800	Weak transcription	K562	blood
2	chr7:4756400-4776800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:4757200-4778800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:4761800-4768000	Enhancers	Fetal Heart	heart
5	chr7:4764000-4766400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:4764200-4766600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr7:4765200-4769800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:4765400-4766400	Enhancers	Spleen	Spleen
9	chr7:4765400-4766400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr7:4765400-4768600	Enhancers	Brain Substantia Nigra	brain
11	chr7:4765400-4778200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:4765600-4766400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:4765600-4766400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:4765600-4766400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:4765600-4766400	Enhancers	Fetal Muscle Trunk	muscle
16	chr7:4765600-4766400	Enhancers	Left Ventricle	heart
17	chr7:4765600-4766400	Enhancers	Right Ventricle	heart
18	chr7:4765600-4766600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr7:4765600-4766600	Enhancers	Fetal Muscle Leg	muscle
20	chr7:4765600-4766600	Enhancers	Lung	lung
21	chr7:4765600-4766600	Enhancers	Right Atrium	heart
22	chr7:4765600-4766800	Enhancers	Brain Anterior Caudate	brain
23	chr7:4765600-4767000	Weak transcription	Placenta	Placenta
24	chr7:4765600-4767200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:4765600-4767200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:4765600-4767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:4765600-4767200	Weak transcription	Fetal Intestine Large	intestine
28	chr7:4765600-4767200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:4765600-4767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:4765600-4767400	Weak transcription	Colonic Mucosa	Colon
31	chr7:4765600-4769800	Weak transcription	Gastric	stomach
32	chr7:4765600-4769800	Weak transcription	Thymus	Thymus
33	chr7:4765600-4770000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr7:4765600-4770000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr7:4765600-4771600	Weak transcription	NHEK	skin
36	chr7:4765600-4773200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:4765600-4777600	Strong transcription	Fetal Intestine Small	intestine
38	chr7:4765600-4778200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr7:4765600-4778200	Weak transcription	Aorta	Aorta
40	chr7:4765600-4778200	Weak transcription	Ovary	ovary
41	chr7:4765600-4778400	Weak transcription	Brain Germinal Matrix	brain
42	chr7:4765600-4783200	Weak transcription	Fetal Brain Male	brain
43	chr7:4765600-4784000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr7:4765800-4766400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr7:4765800-4766400	Enhancers	Duodenum Mucosa	Duodenum
46	chr7:4765800-4766400	Enhancers	HUVEC	blood vessel
47	chr7:4765800-4766600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr7:4765800-4766600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:4765800-4766600	Enhancers	Colon Smooth Muscle	Colon
50	chr7:4765800-4766800	Enhancers	Primary monocytes fromperipheralblood	blood

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