Variant report

Variant	rs4639796
Chromosome Location	chr1:197126649-197126650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197126302..197127851-chr1:197131460..197133305,2	K562	blood:
2	chr1:197121011..197127851-chr1:197128597..197135190,9	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10737686	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10801582	0.85[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs10801586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10922162	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10922167	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10922168	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10922177	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10922179	0.87[EUR][1000 genomes]
rs12028827	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];1.00[ASN][1000 genomes]
rs12034362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12042442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12075161	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12085377	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12116643	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs12128631	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];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134960	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12137359	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]
rs1332660	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1337007	1.00[YRI][hapmap]
rs2298883	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4915344	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5993	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs61819092	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72738632	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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
rs4639796	CFH	cis	parietal	SCAN
rs4639796	CFHR2	cis	cerebellum	SCAN
rs4639796	F13B	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116400-197126800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr1:197116400-197126800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:197116400-197127000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:197116400-197127400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:197116400-197127400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:197116400-197127400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:197116400-197127600	Weak transcription	Brain Germinal Matrix	brain
8	chr1:197116400-197127600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:197116400-197127600	Weak transcription	HSMM	muscle
10	chr1:197116400-197127800	Weak transcription	Fetal Lung	lung
11	chr1:197116400-197127800	Weak transcription	NH-A	brain
12	chr1:197116400-197128000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:197116400-197128200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:197116400-197128200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:197116400-197128400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:197116400-197128400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:197116400-197128400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:197116400-197128400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:197116400-197128400	Weak transcription	Brain Anterior Caudate	brain
20	chr1:197116400-197128400	Weak transcription	Fetal Thymus	thymus
21	chr1:197116400-197128400	Weak transcription	A549	lung
22	chr1:197116400-197128600	Weak transcription	Left Ventricle	heart
23	chr1:197116400-197132000	Weak transcription	HSMMtube	muscle
24	chr1:197116400-197134800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:197116400-197138800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:197116400-197142200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:197116400-197142200	Weak transcription	HUVEC	blood vessel
28	chr1:197116400-197142400	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:197116400-197142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:197116400-197142600	Weak transcription	Fetal Brain Female	brain
31	chr1:197116400-197146200	Weak transcription	Gastric	stomach
32	chr1:197116400-197155000	Weak transcription	Fetal Brain Male	brain
33	chr1:197116600-197127400	Weak transcription	Primary B cells from cord blood	blood
34	chr1:197116600-197127400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:197116600-197127600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:197116600-197127800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:197116600-197128000	Weak transcription	Placenta	Placenta
38	chr1:197116600-197128200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:197116600-197128400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:197116600-197128400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:197116600-197128400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:197116600-197128400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:197116600-197128400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:197116600-197128400	Weak transcription	Adipose Nuclei	Adipose
45	chr1:197116600-197128400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:197116600-197135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:197116600-197142600	Weak transcription	HMEC	breast
48	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:197116800-197128000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:197116800-197128200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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