Variant report

Variant	rs1390735
Chromosome Location	chr6:38034464-38034465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38033550..38035424-chr6:38486236..38488883,2	MCF-7	breast:
2	chr6:38025431..38030854-chr6:38032452..38035354,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12191440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12194872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206687	0.96[ASN][1000 genomes]
rs12524157	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1472364	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.83[MKK][hapmap]
rs1814130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2201646	0.81[TSI][hapmap]
rs259678	0.81[TSI][hapmap]
rs4711519	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6915506	0.81[TSI][hapmap]
rs6929371	0.81[TSI][hapmap]
rs6933547	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs72852542	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765798	0.83[TSI][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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1390735	KCNK5	cis	cerebellum	SCAN
rs1390735	KCNK17	cis	parietal	SCAN
rs1390735	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38017200-38055000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38020400-38046200	Weak transcription	Stomach Mucosa	stomach
3	chr6:38023000-38054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:38023200-38052800	Weak transcription	Gastric	stomach
5	chr6:38024400-38040000	Weak transcription	Fetal Heart	heart
6	chr6:38024600-38035200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:38024600-38041800	Weak transcription	Fetal Brain Male	brain
8	chr6:38024600-38045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:38026000-38035200	Weak transcription	Brain Substantia Nigra	brain
10	chr6:38026000-38047600	Weak transcription	Hela-S3	cervix
11	chr6:38026200-38053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:38028400-38036800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:38029600-38035200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:38030000-38034800	Weak transcription	Ovary	ovary
15	chr6:38030000-38035200	Weak transcription	Small Intestine	intestine
16	chr6:38030400-38037800	Weak transcription	Pancreas	Pancrea
17	chr6:38030600-38035600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:38030600-38035800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:38030800-38036000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:38030800-38036600	Weak transcription	Fetal Intestine Small	intestine
21	chr6:38030800-38041600	Weak transcription	HMEC	breast
22	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:38031000-38034800	Weak transcription	Psoas Muscle	Psoas
24	chr6:38031400-38035200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:38031400-38035600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:38031400-38039400	Weak transcription	K562	blood
27	chr6:38031400-38042400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:38031400-38045000	Weak transcription	Aorta	Aorta
29	chr6:38031400-38052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:38031600-38034800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:38031600-38035200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:38031600-38035200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:38031600-38035600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:38031600-38035800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:38031600-38037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:38031600-38039800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:38031600-38048200	Weak transcription	HUVEC	blood vessel
38	chr6:38031600-38048600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:38031600-38049400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:38031600-38053200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:38031600-38059600	Weak transcription	Spleen	Spleen
42	chr6:38031600-38061600	Weak transcription	Brain Germinal Matrix	brain
43	chr6:38031800-38036600	Weak transcription	Fetal Lung	lung
44	chr6:38031800-38045400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:38032000-38036400	Enhancers	Thymus	Thymus
46	chr6:38032000-38052600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:38032000-38052600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:38032200-38034600	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:38032200-38034800	Weak transcription	Left Ventricle	heart
50	chr6:38032200-38035200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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