Variant report

Variant	rs11888819
Chromosome Location	chr2:36714954-36714955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36708521..36710689-chr2:36714441..36716853,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1179500	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11886869	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890094	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893748	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403857	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403858	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17018901	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021870	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2022210	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770839	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770844	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770845	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3899034	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670562	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60970158	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61077474	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs711249	0.91[CEU][hapmap]
rs7571231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571475	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598753	0.98[ASN][1000 genomes]
rs848530	0.91[CEU][hapmap]
rs848533	0.82[CEU][hapmap]
rs848537	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs848538	0.86[CEU][hapmap]
rs848541	0.83[EUR][1000 genomes]
rs950420	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955601	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][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	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv581468	chr2:36687111-36715689	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11888819	RASGRP3	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36688600-36725600	Weak transcription	Small Intestine	intestine
2	chr2:36703200-36717200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:36704400-36716200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:36704800-36736200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:36705000-36743200	Weak transcription	Brain Germinal Matrix	brain
6	chr2:36707000-36740600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:36707400-36716400	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:36707600-36716600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:36707600-36717000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:36708600-36739000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:36708800-36720800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:36708800-36726000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:36709000-36719600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:36709200-36726800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:36709200-36727200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:36709200-36739000	Weak transcription	Colonic Mucosa	Colon
17	chr2:36709400-36726600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:36709400-36726800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:36709400-36726800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:36710000-36743400	Weak transcription	Primary T cells from cord blood	blood
21	chr2:36710400-36726600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:36711200-36717400	Enhancers	Rectal Smooth Muscle	rectum
23	chr2:36711200-36726600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:36711400-36715600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:36711400-36726400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:36711400-36726400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:36711400-36726600	Weak transcription	Esophagus	oesophagus
28	chr2:36711400-36739200	Weak transcription	Primary B cells from cord blood	blood
29	chr2:36711600-36716400	Genic enhancers	Hela-S3	cervix
30	chr2:36711600-36726800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:36711800-36717200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:36711800-36717600	Weak transcription	Lung	lung
33	chr2:36711800-36726400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:36712000-36715200	Enhancers	Fetal Heart	heart
35	chr2:36712000-36715200	Enhancers	NHLF	lung
36	chr2:36712000-36715400	Weak transcription	Fetal Intestine Small	intestine
37	chr2:36712000-36715800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr2:36712000-36717200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:36712000-36720000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:36712000-36726400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:36712000-36726400	Weak transcription	Spleen	Spleen
42	chr2:36712000-36726600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:36712000-36726600	Weak transcription	Gastric	stomach
44	chr2:36712400-36715400	Enhancers	Fetal Kidney	kidney
45	chr2:36712400-36718400	Enhancers	HSMMtube	muscle
46	chr2:36712600-36715000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:36712600-36715400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:36712600-36715400	Enhancers	NH-A	brain
49	chr2:36712600-36715800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:36712600-36715800	Enhancers	HMEC	breast

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