Variant report

Variant	rs7771115
Chromosome Location	chr6:56961521-56961522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56959009..56963624-chr6:57035365..57039055,4	K562	blood:
2	chr12:77457691..77459253-chr6:56958727..56961580,2	MCF-7	breast:
3	chr6:56954768..56956361-chr6:56959991..56962097,2	MCF-7	breast:
4	chr6:56959161..56962012-chr6:57000090..57002565,2	K562	blood:
5	chr6:56960085..56961933-chr6:57032456..57035012,2	K562	blood:

Variant related genes	Relation type
ENSG00000112200	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1020550	0.90[ASN][1000 genomes]
rs1044670	0.88[CEU][hapmap]
rs10456192	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][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];0.96[EUR][1000 genomes];1.00[ASN][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];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12190575	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192222	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194288	0.90[ASN][1000 genomes]
rs12194407	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198801	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201039	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12214119	0.95[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][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[AMR][1000 genomes];0.90[ASN][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];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs3800023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3957366	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs3996934	0.90[ASN][1000 genomes]
rs3996935	0.90[ASN][1000 genomes]
rs3996936	0.90[ASN][1000 genomes]
rs4523090	0.90[ASN][1000 genomes]
rs4631287	0.90[ASN][1000 genomes]
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];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6918222	0.86[EUR][1000 genomes]
rs6936506	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936560	0.81[EUR][1000 genomes]
rs72868608	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73463742	0.80[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7753547	0.90[ASN][1000 genomes]
rs7756421	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]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9349841	0.85[ASN][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9396256	0.90[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7771115	BEND6	cis	parietal	SCAN
rs7771115	BEND6	cis	cerebellum	SCAN
rs7771115	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs7771115	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs7771115	BEND6	cis	Muscle Skeletal	GTEx
rs7771115	RAB23	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56954000-56966800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56955200-56961600	Weak transcription	Lung	lung
3	chr6:56955200-56961800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:56955200-56962200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:56955200-56962800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56955200-56963800	Weak transcription	Colonic Mucosa	Colon
7	chr6:56955200-56964200	Weak transcription	Psoas Muscle	Psoas
8	chr6:56955200-56964400	Weak transcription	Pancreas	Pancrea
9	chr6:56955200-56964400	Weak transcription	Spleen	Spleen
10	chr6:56955200-56965400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:56955200-56965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:56955200-56965800	Weak transcription	Esophagus	oesophagus
13	chr6:56956600-56961600	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:56956600-56965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:56956600-56965600	Weak transcription	Gastric	stomach
16	chr6:56956800-56963800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:56957000-56962000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:56957000-56962000	Weak transcription	HSMMtube	muscle
19	chr6:56957000-56963400	Weak transcription	Thymus	Thymus
20	chr6:56957000-56963800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:56957000-56964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:56957000-56964400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:56957000-56965200	Weak transcription	Small Intestine	intestine
24	chr6:56957000-56965400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:56957000-56965800	Weak transcription	Stomach Mucosa	stomach
26	chr6:56957200-56962000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:56957200-56962000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:56957200-56962200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:56957200-56963000	Weak transcription	Fetal Lung	lung
30	chr6:56957200-56963200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:56957200-56963800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:56957400-56963000	Weak transcription	NHLF	lung
33	chr6:56957400-56963600	Weak transcription	Fetal Kidney	kidney
34	chr6:56957600-56962200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:56957600-56967600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:56957800-56962000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:56957800-56963200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:56957800-56963200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:56957800-56963800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:56957800-56964400	Weak transcription	Fetal Brain Male	brain
41	chr6:56957800-56965400	Weak transcription	Right Ventricle	heart
42	chr6:56958000-56963400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:56958000-56964200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:56958200-56961800	Weak transcription	Placenta	Placenta
45	chr6:56958200-56961800	Weak transcription	HSMM	muscle
46	chr6:56958200-56962400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:56958200-56963200	Weak transcription	Brain Germinal Matrix	brain
48	chr6:56958200-56963400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:56958200-56979600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:56958400-56961800	Weak transcription	Brain Anterior Caudate	brain

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