Variant report

Variant	rs7744316
Chromosome Location	chr6:57081878-57081879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57080840..57082860-chr6:57084756..57087853,3	MCF-7	breast:
2	chr6:57072490..57076553-chr6:57079745..57082714,5	K562	blood:
3	chr6:57033881..57038745-chr6:57081255..57088571,10	K562	blood:
4	chr6:57072490..57075602-chr6:57079745..57082698,3	K562	blood:
5	chr6:57036968..57040373-chr6:57081738..57084923,6	K562	blood:
6	chr6:57080126..57084455-chr6:57085669..57087997,5	K562	blood:

Variant related genes	Relation type
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000112210	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1157713	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs12190416	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs12190434	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12192711	0.96[ASN][1000 genomes]
rs12210597	1.00[CEU][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211611	0.82[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16888392	0.81[CEU][hapmap];0.90[TSI][hapmap]
rs2273921	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3734738	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs3778515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs3800018	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs3800019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996929	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6459180	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6913707	0.85[ASN][1000 genomes]
rs6926980	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6928715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs6929783	0.85[ASN][1000 genomes]
rs6936472	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[ASN][1000 genomes]
rs7743855	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7744824	0.94[ASN][1000 genomes]
rs7753537	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7753927	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7763570	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8180538	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9349843	0.93[ASN][1000 genomes]
rs9367704	1.00[JPT][hapmap]
rs9367708	0.93[ASN][1000 genomes]
rs9370564	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs9370565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9382680	0.80[YRI][hapmap]
rs9382689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9396259	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs952647	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs9885757	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7744316	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs7744316	RAB23	cis	multi-tissue	Pritchard
rs7744316	BEND6	cis	parietal	SCAN
rs7744316	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs7744316	BEND6	cis	cerebellum	SCAN
rs7744316	RAB23	cis	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
2	chr6:57049400-57085000	Weak transcription	Aorta	Aorta
3	chr6:57056600-57086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:57058200-57085800	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:57058800-57084000	Weak transcription	Dnd41	blood
6	chr6:57059200-57084000	Weak transcription	Hela-S3	cervix
7	chr6:57062600-57084800	Weak transcription	HSMM	muscle
8	chr6:57064400-57084000	Weak transcription	NH-A	brain
9	chr6:57064400-57085000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:57064400-57086200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:57065000-57085000	Weak transcription	A549	lung
12	chr6:57067600-57085800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:57070600-57086000	Weak transcription	HSMMtube	muscle
14	chr6:57071600-57084800	Weak transcription	HUVEC	blood vessel
15	chr6:57072000-57085800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:57078200-57083000	Weak transcription	HepG2	liver
17	chr6:57078200-57086000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:57078600-57083200	Enhancers	Rectal Smooth Muscle	rectum
19	chr6:57079200-57084200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:57079400-57084400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:57079400-57085600	Weak transcription	Fetal Stomach	stomach
22	chr6:57079400-57086000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:57079600-57083600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:57079600-57084000	Weak transcription	NHLF	lung
25	chr6:57079600-57086200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:57079800-57084800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:57080000-57085000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:57080200-57086000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:57080200-57086000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:57080200-57086000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr6:57080600-57082000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:57080800-57082000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:57080800-57082000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:57080800-57082000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:57081200-57082000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:57081200-57082000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:57081200-57082000	Enhancers	HMEC	breast
38	chr6:57081200-57082400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:57081200-57082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:57081200-57085800	Weak transcription	Fetal Lung	lung
41	chr6:57081200-57085800	Weak transcription	Right Atrium	heart
42	chr6:57081400-57082000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:57081600-57082000	Enhancers	GM12878-XiMat	blood
44	chr6:57081600-57082400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:57081600-57086000	Weak transcription	Ovary	ovary
46	chr6:57081800-57082400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:57081800-57082400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:57081800-57082600	Enhancers	NHEK	skin
49	chr6:57081800-57082800	Enhancers	Osteobl	bone
50	chr6:57081800-57083000	Active TSS	K562	blood

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