Variant report

Variant	rs10490657
Chromosome Location	chr2:37178255-37178256
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	chr2:37172866..37175406-chr2:37175824..37179648,3	K562	blood:
2	chr2:37177111..37181482-chr2:37191828..37195720,6	K562	blood:

Variant related genes	Relation type
ENSG00000115808	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10193295	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11124554	0.81[ASN][1000 genomes]
rs11124555	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11679564	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11695609	0.96[ASN][1000 genomes]
rs12476515	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13418962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17020071	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs17443495	1.00[JPT][hapmap]
rs17497343	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003585	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2110994	0.85[ASN][1000 genomes]
rs2252032	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2372786	0.90[ASN][1000 genomes]
rs2540998	0.84[CHB][hapmap]
rs2691106	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2717493	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3770774	0.89[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3845778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3845780	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4016033	0.80[ASN][1000 genomes]
rs4016036	0.90[ASN][1000 genomes]
rs4389320	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45504994	0.80[ASN][1000 genomes]
rs4670637	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670638	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57747847	0.80[ASN][1000 genomes]
rs62133068	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62135860	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6752845	0.82[JPT][hapmap]
rs7560263	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7573966	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7588378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7605601	0.85[ASN][1000 genomes]
rs888083	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv961397	chr2:37173966-37180387	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10490657	STRN	cis	multi-tissue	Pritchard
rs10490657	EIF2AK2	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37132400-37192400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:37134600-37192400	Weak transcription	Fetal Stomach	stomach
3	chr2:37136400-37178800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:37142000-37178400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:37142000-37178800	Weak transcription	Primary B cells from cord blood	blood
6	chr2:37143400-37191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:37143800-37191800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:37150200-37191800	Weak transcription	Fetal Thymus	thymus
9	chr2:37152400-37191800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:37154000-37178400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:37154200-37179400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:37154600-37178800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:37154600-37179000	Weak transcription	Esophagus	oesophagus
14	chr2:37154600-37191800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:37154800-37178800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:37154800-37185600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:37155000-37183600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:37158000-37183600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:37158200-37178800	Weak transcription	Left Ventricle	heart
20	chr2:37158200-37192000	Weak transcription	Ovary	ovary
21	chr2:37158400-37178400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:37158600-37191800	Weak transcription	Fetal Lung	lung
23	chr2:37159000-37191800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:37163600-37178400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:37164800-37178800	Weak transcription	Lung	lung
26	chr2:37165000-37190800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:37165200-37178400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:37165600-37179000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:37165600-37191800	Weak transcription	Fetal Intestine Small	intestine
30	chr2:37166600-37191600	Weak transcription	Dnd41	blood
31	chr2:37168600-37191800	Weak transcription	Thymus	Thymus
32	chr2:37169600-37179000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:37169800-37178400	Weak transcription	Right Ventricle	heart
34	chr2:37169800-37186800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:37170000-37178400	Weak transcription	K562	blood
36	chr2:37170400-37178400	Weak transcription	Gastric	stomach
37	chr2:37170600-37178400	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:37172400-37178400	Weak transcription	Fetal Heart	heart
39	chr2:37176200-37191800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:37176400-37183800	Weak transcription	HepG2	liver
41	chr2:37176800-37180400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr2:37177000-37179600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:37177000-37182200	Weak transcription	GM12878-XiMat	blood
44	chr2:37177200-37180000	Enhancers	HUVEC	blood vessel
45	chr2:37177200-37180200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:37177400-37179000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:37177600-37178400	Weak transcription	Psoas Muscle	Psoas
48	chr2:37177600-37178800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:37177600-37178800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:37177600-37179200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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