Variant report

Variant	rs6910832
Chromosome Location	chr6:36856739-36856740
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36856213..36857757-chr6:36880453..36883073,2	MCF-7	breast:
2	chr6:36855815..36857675-chr6:36943714..36945345,2	K562	blood:
3	chr6:36829835..36831683-chr6:36855504..36857194,2	K562	blood:
4	chr6:36852175..36855710-chr6:36855896..36859725,4	MCF-7	breast:
5	chr6:36816600..36820003-chr6:36855117..36857436,3	K562	blood:
6	chr6:36856383..36858812-chr6:36892219..36894904,2	K562	blood:
7	chr6:36856253..36859191-chr6:36932885..36935045,2	K562	blood:
8	chr6:36854706..36858515-chr6:36943714..36946707,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1022696	0.84[YRI][hapmap]
rs10947647	0.84[YRI][hapmap]
rs1150784	0.90[ASN][1000 genomes]
rs11759850	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2116447	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs2272275	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs2272276	0.91[LWK][hapmap];0.84[YRI][hapmap]
rs2293393	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2303993	0.96[ASN][1000 genomes]
rs236349	0.81[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs236352	0.92[ASN][1000 genomes]
rs236358	0.80[JPT][hapmap]
rs236385	0.84[JPT][hapmap]
rs236386	0.84[JPT][hapmap]
rs2395663	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs3756905	0.96[ASN][1000 genomes]
rs3778016	0.96[ASN][1000 genomes]
rs3778017	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3846871	0.91[ASN][1000 genomes]
rs3957238	0.92[YRI][hapmap]
rs449840	0.94[ASN][1000 genomes]
rs460539	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4711471	0.84[EUR][1000 genomes]
rs4711473	0.81[AFR][1000 genomes]
rs4714018	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58214515	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62406643	0.92[ASN][1000 genomes]
rs6457963	0.87[ASN][1000 genomes]
rs6909988	0.96[ASN][1000 genomes]
rs6914008	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6932175	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs6934844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743646	0.83[LWK][hapmap];0.88[YRI][hapmap]
rs7743836	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs7761653	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs7774420	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs831480	0.86[CHB][hapmap]
rs8472	0.88[ASN][1000 genomes]
rs9296200	0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs9349017	0.88[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs9366917	0.84[JPT][hapmap]
rs9366920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368966	0.94[ASN][1000 genomes]
rs9380616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380618	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9380626	0.84[ASN][1000 genomes]
rs9462238	0.80[AFR][1000 genomes]
rs9462240	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs9462241	0.84[YRI][hapmap]
rs9470426	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6910832	TCP11	cis	cerebellum	SCAN
rs6910832	SRPK1	cis	cerebellum	SCAN
rs6910832	STK38	cis	cerebellum	SCAN
rs6910832	PNPLA1	cis	parietal	SCAN
rs6910832	PPIL1	Cis_1M	lymphoblastoid	RTeQTL
rs6910832	LRFN2	cis	cerebellum	SCAN
rs6910832	SPDEF	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36860200	Weak transcription	Spleen	Spleen
2	chr6:36854200-36862200	Weak transcription	Lung	lung
3	chr6:36854200-36868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36854200-36873600	Weak transcription	Aorta	Aorta
5	chr6:36854200-36881000	Weak transcription	Gastric	stomach
6	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:36854400-36858000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:36854400-36860200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:36854400-36868400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:36854600-36857400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:36854600-36859800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:36854600-36869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:36854600-36870000	Weak transcription	Stomach Mucosa	stomach
15	chr6:36854800-36856800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:36854800-36857000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:36854800-36858000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:36854800-36858200	Enhancers	Fetal Heart	heart
19	chr6:36854800-36860000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:36854800-36860000	Weak transcription	Fetal Stomach	stomach
21	chr6:36854800-36861400	Weak transcription	Placenta	Placenta
22	chr6:36854800-36866600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:36854800-36868400	Weak transcription	Brain Germinal Matrix	brain
24	chr6:36854800-36870000	Weak transcription	Colonic Mucosa	Colon
25	chr6:36854800-36875200	Weak transcription	Esophagus	oesophagus
26	chr6:36854800-36881000	Weak transcription	A549	lung
27	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:36855000-36859800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:36855000-36859800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:36855000-36859800	Weak transcription	Fetal Intestine Small	intestine
32	chr6:36855000-36859800	Weak transcription	Osteobl	bone
33	chr6:36855000-36860000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:36855000-36860000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:36855000-36860000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:36855000-36860000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:36855000-36862000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr6:36855000-36862200	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:36855000-36862200	Weak transcription	Fetal Intestine Large	intestine
40	chr6:36855000-36862200	Weak transcription	HMEC	breast
41	chr6:36855000-36862200	Weak transcription	HSMM	muscle
42	chr6:36855000-36862200	Weak transcription	HSMMtube	muscle
43	chr6:36855000-36866600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:36855000-36866600	Weak transcription	HUVEC	blood vessel
45	chr6:36855000-36866800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:36855000-36866800	Weak transcription	Fetal Kidney	kidney
47	chr6:36855000-36867200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:36855200-36859800	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:36855200-36862000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr6:36855200-36862200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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