Variant report

Variant	rs7756421
Chromosome Location	chr6:57034009-57034010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56960085..56961933-chr6:57032456..57035012,2	K562	blood:
2	chr6:57033881..57038745-chr6:57081255..57088571,10	K562	blood:
3	chr6:57033399..57035837-chr6:57077480..57080109,2	K562	blood:
4	chr6:57031801..57034883-chr6:57035527..57038965,3	MCF-7	breast:

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

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1044670	0.88[CEU][hapmap]
rs10456192	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10484410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11398	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12190575	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12192222	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12194407	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12198801	0.83[EUR][1000 genomes]
rs12201039	0.98[EUR][1000 genomes]
rs12211901	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12214882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16888392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17619360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3800018	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs3800023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3957366	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs6459178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6936506	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72868608	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7748120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7771115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	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
6	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
rs7756421	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs7756421	RAB23	cis	lymphoblastoid	seeQTL
rs7756421	BEND6	cis	parietal	SCAN
rs7756421	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs7756421	BEND6	cis	Muscle Skeletal	GTEx
rs7756421	BEND6	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:56985600-57036800	Weak transcription	Pancreas	Pancrea
3	chr6:56991600-57036600	Weak transcription	Small Intestine	intestine
4	chr6:56995800-57036600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56996000-57036800	Weak transcription	Gastric	stomach
6	chr6:56996200-57036600	Weak transcription	Fetal Brain Male	brain
7	chr6:56996400-57036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:56999800-57036600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:57001200-57036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:57002600-57036600	Weak transcription	A549	lung
11	chr6:57006600-57036600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:57011400-57036600	Weak transcription	Stomach Mucosa	stomach
13	chr6:57012400-57036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:57012800-57036400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:57012800-57036600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:57013200-57036600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:57013600-57036000	Weak transcription	Fetal Heart	heart
18	chr6:57016000-57036600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:57018800-57036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:57019000-57036400	Weak transcription	Fetal Stomach	stomach
21	chr6:57019000-57036400	Weak transcription	Lung	lung
22	chr6:57019000-57036600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:57019000-57036600	Weak transcription	Aorta	Aorta
24	chr6:57019000-57036600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:57019000-57036800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:57019400-57034400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:57019400-57036400	Weak transcription	Ovary	ovary
28	chr6:57019400-57036400	Weak transcription	Thymus	Thymus
29	chr6:57020400-57036600	Weak transcription	Colonic Mucosa	Colon
30	chr6:57020400-57036600	Weak transcription	Fetal Intestine Small	intestine
31	chr6:57020400-57036800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:57020600-57036400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:57021400-57036600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:57021600-57036800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:57021800-57036600	Weak transcription	Right Ventricle	heart
36	chr6:57021800-57036800	Weak transcription	Esophagus	oesophagus
37	chr6:57026400-57036800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:57026600-57036200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:57026800-57036800	Weak transcription	Left Ventricle	heart
40	chr6:57027200-57035600	Strong transcription	Placenta	Placenta
41	chr6:57027400-57036600	Weak transcription	HUVEC	blood vessel
42	chr6:57028000-57036200	Weak transcription	Hela-S3	cervix
43	chr6:57028200-57036200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:57028200-57036600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:57028200-57036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:57028600-57035400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:57029200-57036200	Weak transcription	Fetal Thymus	thymus
48	chr6:57029200-57036400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:57030000-57036400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:57030200-57036400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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