Variant report

Variant	rs4680282
Chromosome Location	chr3:156250797-156250798
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156234016..156236952-chr3:156250322..156252115,2	K562	blood:
2	chr3:156249802..156251861-chr3:156257481..156258995,2	MCF-7	breast:
3	chr3:156250031..156252354-chr3:156394197..156396379,2	K562	blood:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1027915	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10513493	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1129109	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1510277	0.94[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1510278	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907060	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs908807	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9820091	0.94[CEU][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9856073	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4680282	KCNAB1	Cis_1M	lymphoblastoid	RTeQTL
rs4680282	SSR3	Cis_1M	lymphoblastoid	RTeQTL
rs4680282	LXN	cis	parietal	SCAN
rs4680282	C3orf33	cis	cerebellum	SCAN
rs4680282	KCNAB1	cis	multi-tissue	Pritchard

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156230200-156251000	Weak transcription	Left Ventricle	heart
2	chr3:156234400-156251200	Weak transcription	Ovary	ovary
3	chr3:156236800-156251000	Weak transcription	Pancreas	Pancrea
4	chr3:156236800-156251200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:156238200-156251400	Weak transcription	A549	lung
6	chr3:156240400-156260200	Weak transcription	Esophagus	oesophagus
7	chr3:156240600-156251800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:156241600-156250800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:156241600-156255800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:156241800-156251000	Weak transcription	HSMMtube	muscle
11	chr3:156242000-156253000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:156242200-156251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:156243000-156255200	Weak transcription	Dnd41	blood
14	chr3:156243200-156251000	Weak transcription	HSMM	muscle
15	chr3:156243200-156253800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:156243200-156255600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:156243200-156255600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:156243200-156255800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:156243200-156256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:156243200-156256800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:156243200-156256800	Weak transcription	GM12878-XiMat	blood
22	chr3:156243200-156257000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:156243200-156257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:156243200-156258800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:156243400-156256600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:156243400-156256800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:156244000-156257000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:156244400-156253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:156244600-156257000	Weak transcription	Lung	lung
30	chr3:156244800-156252200	Weak transcription	NHLF	lung
31	chr3:156245000-156257000	Weak transcription	Spleen	Spleen
32	chr3:156245400-156257200	Weak transcription	Fetal Brain Male	brain
33	chr3:156246000-156253200	Weak transcription	Fetal Stomach	stomach
34	chr3:156246600-156252800	Weak transcription	Liver	Liver
35	chr3:156246800-156252800	Weak transcription	Fetal Intestine Small	intestine
36	chr3:156246800-156263600	Weak transcription	Fetal Brain Female	brain
37	chr3:156247000-156251200	Weak transcription	Aorta	Aorta
38	chr3:156247200-156253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:156247200-156263800	Weak transcription	Thymus	Thymus
40	chr3:156247600-156257200	Weak transcription	Hela-S3	cervix
41	chr3:156247800-156252800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:156247800-156253000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:156248000-156257000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:156248200-156251200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:156248400-156251000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:156248600-156251000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:156248800-156257000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:156249000-156264600	Weak transcription	Brain Germinal Matrix	brain
49	chr3:156249400-156251000	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:156249400-156252200	Weak transcription	Brain Anterior Caudate	brain

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