Variant report

Variant	rs1187421
Chromosome Location	chr6:37809880-37809881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37786218..37789044-chr6:37808476..37810682,2	MCF-7	breast:
2	chr6:37785007..37788077-chr6:37806968..37810692,5	K562	blood:
3	chr6:37799938..37802432-chr6:37807821..37809995,2	K562	blood:
4	chr6:37797940..37799807-chr6:37808764..37811623,2	MCF-7	breast:
5	chr6:37785007..37788077-chr6:37806355..37810692,7	K562	blood:
6	chr6:37802711..37804366-chr6:37809800..37811727,2	K562	blood:
7	chr6:37790878..37792753-chr6:37808430..37810032,2	K562	blood:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000243313	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10485029	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1074234	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947707	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1187422	0.91[AFR][1000 genomes]
rs1187423	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12190570	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200258	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs12211248	0.89[CHB][hapmap];0.84[AFR][1000 genomes]
rs12211981	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs12213835	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs13210701	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs2055206	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259679	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259686	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs259689	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs259690	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs259691	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs259713	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs259715	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs259716	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs259718	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645107	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs2645116	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs2645117	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2645124	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[ASN][1000 genomes]
rs2842517	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs2842527	1.00[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.80[MEX][hapmap];0.96[YRI][hapmap]
rs34592529	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35806631	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35925070	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4714117	0.81[CHB][hapmap]
rs4714120	0.81[CHB][hapmap];0.85[TSI][hapmap]
rs6458028	0.83[AFR][1000 genomes]
rs6458029	0.85[CEU][hapmap]
rs9296232	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs9394460	0.93[ASW][hapmap];0.85[CEU][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.81[AFR][1000 genomes]
rs9470706	0.88[EUR][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	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	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1187421	KCNK17	cis	parietal	SCAN
rs1187421	MDGA1	cis	cerebellum	SCAN
rs1187421	GLO1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37791200-37820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:37791400-37810200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:37791400-37813400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:37791400-37816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:37793800-37813600	Weak transcription	NH-A	brain
6	chr6:37794000-37819800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:37795000-37813800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:37795000-37825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:37795800-37813400	Weak transcription	HSMMtube	muscle
10	chr6:37796000-37812800	Weak transcription	Colonic Mucosa	Colon
11	chr6:37796000-37813200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:37796000-37813800	Weak transcription	NHDF-Ad	bronchial
13	chr6:37796000-37815600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:37796000-37828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:37796000-37830600	Weak transcription	Hela-S3	cervix
16	chr6:37796200-37811400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:37796200-37813200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:37798400-37812800	Weak transcription	HSMM	muscle
19	chr6:37798400-37815200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:37798400-37815800	Weak transcription	Fetal Heart	heart
21	chr6:37799400-37817400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:37799600-37811200	Weak transcription	Brain Substantia Nigra	brain
23	chr6:37799600-37811800	Weak transcription	Placenta	Placenta
24	chr6:37799600-37812800	Weak transcription	NHEK	skin
25	chr6:37799600-37813400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:37799600-37825800	Weak transcription	Esophagus	oesophagus
27	chr6:37799800-37825400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:37800200-37812800	Weak transcription	Gastric	stomach
29	chr6:37800200-37813400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:37800200-37830200	Weak transcription	Ovary	ovary
31	chr6:37800200-37836200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:37800400-37813200	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:37801000-37811400	Weak transcription	Thymus	Thymus
34	chr6:37801000-37811600	Weak transcription	Fetal Thymus	thymus
35	chr6:37801000-37811800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:37801000-37813600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:37801000-37817600	Weak transcription	Spleen	Spleen
38	chr6:37801000-37818600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:37801200-37833400	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:37802200-37812800	Weak transcription	A549	lung
41	chr6:37802400-37810000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:37802400-37811600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:37802400-37811600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr6:37802400-37812800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:37802400-37813200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:37802400-37813200	Weak transcription	Fetal Kidney	kidney
47	chr6:37802400-37818400	Weak transcription	Primary B cells from cord blood	blood
48	chr6:37802600-37812200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:37802600-37818400	Weak transcription	Fetal Lung	lung
50	chr6:37802600-37834400	Weak transcription	Duodenum Mucosa	Duodenum

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