Variant report

Variant	rs12137359
Chromosome Location	chr1:197129981-197129982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197121011..197127851-chr1:197128597..197135190,9	K562	blood:
2	chr1:197128463..197130578-chr1:197135579..197137702,2	K562	blood:
3	chr1:197112460..197117731-chr1:197129268..197134426,6	K562	blood:

Variant related genes	Relation type
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10737686	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10801582	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs10801586	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10922162	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10922167	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10922168	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10922177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10922179	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12028827	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034362	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12042442	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12075161	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12085377	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12116643	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs12128631	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12134960	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1332660	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332664	0.80[EUR][1000 genomes]
rs1337007	1.00[YRI][hapmap]
rs2298883	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4639796	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4915344	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5993	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61819092	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72738632	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12137359	CFH	cis	parietal	SCAN
rs12137359	F13B	cis	cerebellum	SCAN
rs12137359	CFHR2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116400-197132000	Weak transcription	HSMMtube	muscle
2	chr1:197116400-197134800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:197116400-197138800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:197116400-197142200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:197116400-197142200	Weak transcription	HUVEC	blood vessel
6	chr1:197116400-197142400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:197116400-197142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:197116400-197142600	Weak transcription	Fetal Brain Female	brain
9	chr1:197116400-197146200	Weak transcription	Gastric	stomach
10	chr1:197116400-197155000	Weak transcription	Fetal Brain Male	brain
11	chr1:197116600-197135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:197116600-197142600	Weak transcription	HMEC	breast
13	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:197116800-197143200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:197117000-197142600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:197120400-197130800	Weak transcription	NHDF-Ad	bronchial
17	chr1:197121600-197154800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:197122400-197134800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:197123800-197143200	Weak transcription	Thymus	Thymus
20	chr1:197123800-197147600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:197124200-197136000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:197124200-197140600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:197124200-197143200	Weak transcription	Fetal Heart	heart
24	chr1:197124400-197139600	Weak transcription	GM12878-XiMat	blood
25	chr1:197124600-197142600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:197124600-197155400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:197124800-197139600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:197124800-197144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:197125000-197142400	Weak transcription	Fetal Kidney	kidney
30	chr1:197125200-197141600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:197125200-197142600	Weak transcription	Small Intestine	intestine
32	chr1:197125200-197142800	Weak transcription	NHEK	skin
33	chr1:197125200-197156000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:197125200-197156400	Weak transcription	Right Ventricle	heart
35	chr1:197125400-197155600	Weak transcription	Fetal Stomach	stomach
36	chr1:197125400-197156200	Weak transcription	Pancreas	Pancrea
37	chr1:197125400-197156400	Weak transcription	Aorta	Aorta
38	chr1:197125400-197156400	Weak transcription	Lung	lung
39	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
40	chr1:197125600-197160000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
42	chr1:197125800-197143000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:197125800-197158400	Weak transcription	Spleen	Spleen
44	chr1:197126000-197143000	Weak transcription	Brain Substantia Nigra	brain
45	chr1:197126400-197130200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:197126800-197132200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:197126800-197132400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:197127000-197132400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:197127000-197148200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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