Variant report

Variant	rs1370627
Chromosome Location	chr2:101009385-101009386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:101005691..101009453-chr2:101017314..101020656,3	MCF-7	breast:
2	chr2:101003802..101007409-chr2:101009327..101011119,3	K562	blood:
3	chr2:101004553..101007119-chr2:101009350..101012727,3	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10167159	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172841	0.93[GIH][hapmap]
rs10180570	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10184899	0.88[ASN][1000 genomes]
rs10193535	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10198495	1.00[ASN][1000 genomes]
rs10198682	1.00[ASN][1000 genomes]
rs10200480	1.00[ASN][1000 genomes]
rs10201098	1.00[ASN][1000 genomes]
rs10204833	1.00[ASN][1000 genomes]
rs10206374	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs10208900	1.00[ASN][1000 genomes]
rs10208911	1.00[ASN][1000 genomes]
rs10209186	1.00[ASN][1000 genomes]
rs1057056	1.00[GIH][hapmap]
rs1057063	1.00[EUR][1000 genomes]
rs1107429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1124009	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13391930	0.88[ASN][1000 genomes]
rs13396147	0.88[ASN][1000 genomes]
rs13400841	0.96[GIH][hapmap]
rs13404823	0.88[ASN][1000 genomes]
rs13407408	0.88[ASN][1000 genomes]
rs13407648	0.88[ASN][1000 genomes]
rs13407891	0.88[ASN][1000 genomes]
rs13410582	0.88[ASN][1000 genomes]
rs13419808	0.88[ASN][1000 genomes]
rs13420942	1.00[ASN][1000 genomes]
rs1347721	1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437970	1.00[ASN][1000 genomes]
rs1437972	0.93[GIH][hapmap]
rs17023985	1.00[ASN][1000 genomes]
rs17024035	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs17024129	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs17024133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap]
rs17024136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs17024144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs17024209	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1898571	0.88[ASN][1000 genomes]
rs1898574	1.00[ASN][1000 genomes]
rs2309793	1.00[ASN][1000 genomes]
rs2309801	0.96[GIH][hapmap]
rs3748936	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3791358	0.90[GIH][hapmap]
rs4149509	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4149514	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4149515	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4850932	0.96[GIH][hapmap]
rs55640826	0.88[ASN][1000 genomes]
rs55843950	0.88[ASN][1000 genomes]
rs56051859	1.00[ASN][1000 genomes]
rs56118658	0.88[ASN][1000 genomes]
rs56342384	1.00[ASN][1000 genomes]
rs56656536	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58876304	0.88[ASN][1000 genomes]
rs59340778	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60131548	0.88[ASN][1000 genomes]
rs60609848	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60898093	0.88[ASN][1000 genomes]
rs61321970	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61559573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6542931	1.00[ASN][1000 genomes]
rs6542932	1.00[ASN][1000 genomes]
rs6542939	1.00[ASN][1000 genomes]
rs6542941	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6542946	0.93[GIH][hapmap]
rs6708942	0.88[ASN][1000 genomes]
rs6713862	0.88[ASN][1000 genomes]
rs6714109	1.00[ASN][1000 genomes]
rs6716009	0.88[ASN][1000 genomes]
rs6716367	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724695	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6725672	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6728575	0.93[GIH][hapmap]
rs6732285	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6739576	1.00[ASN][1000 genomes]
rs6739589	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6740098	1.00[ASN][1000 genomes]
rs6750866	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6754379	1.00[ASN][1000 genomes]
rs6754869	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6755395	1.00[ASN][1000 genomes]
rs6757774	0.88[ASN][1000 genomes]
rs6758156	0.88[ASN][1000 genomes]
rs6758161	0.88[ASN][1000 genomes]
rs6758515	0.88[ASN][1000 genomes]
rs6758622	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6761561	0.88[ASN][1000 genomes]
rs72960172	1.00[ASN][1000 genomes]
rs72960184	0.88[ASN][1000 genomes]
rs72960186	0.88[ASN][1000 genomes]
rs72960202	0.88[ASN][1000 genomes]
rs73966107	1.00[ASN][1000 genomes]
rs73966108	1.00[ASN][1000 genomes]
rs73968412	1.00[ASN][1000 genomes]
rs73968415	0.94[ASN][1000 genomes]
rs73968817	1.00[ASN][1000 genomes]
rs7556717	1.00[ASN][1000 genomes]
rs7557137	1.00[ASN][1000 genomes]
rs7559939	0.88[ASN][1000 genomes]
rs7559946	0.88[ASN][1000 genomes]
rs7562461	0.88[ASN][1000 genomes]
rs7562479	0.88[ASN][1000 genomes]
rs7562486	0.88[ASN][1000 genomes]
rs7562615	0.88[ASN][1000 genomes]
rs7564178	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7571659	0.93[GIH][hapmap]
rs7572119	0.88[ASN][1000 genomes]
rs7574684	0.88[ASN][1000 genomes]
rs7575422	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7576749	0.88[ASN][1000 genomes]
rs7582096	0.96[GIH][hapmap]
rs7582546	1.00[CHB][hapmap]
rs7585713	0.96[GIH][hapmap]
rs7585898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs7587333	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597631	1.00[ASN][1000 genomes]
rs7597722	1.00[ASN][1000 genomes]
rs7598205	0.93[GIH][hapmap]
rs7606723	1.00[ASN][1000 genomes]
rs876439	0.93[GIH][hapmap]
rs9308834	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv874701	chr2:100976139-101023261	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1370627	DUSP2	trans	brain	seeQTL
rs1370627	NPAS4	trans	brain	seeQTL
rs1370627	EGR4	trans	brain	seeQTL
rs1370627	PTGS2	trans	brain	seeQTL
rs1370627	FOS	trans	brain	seeQTL
rs1370627	ARC	trans	brain	seeQTL
rs1370627	EGR2	trans	brain	seeQTL
rs1370627	FOSB	trans	brain	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100993200-101017800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:100998200-101022600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:100998400-101010000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:101000400-101009400	Weak transcription	HepG2	liver
5	chr2:101002000-101023400	Weak transcription	Psoas Muscle	Psoas
6	chr2:101002400-101012000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:101003200-101021000	Weak transcription	K562	blood
8	chr2:101005200-101015000	Strong transcription	Fetal Brain Female	brain
9	chr2:101005600-101017600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:101005600-101032800	Weak transcription	HUVEC	blood vessel
11	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:101006000-101021600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:101006400-101018400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:101006600-101023600	Strong transcription	Brain Germinal Matrix	brain
15	chr2:101006600-101031600	Strong transcription	Fetal Stomach	stomach
16	chr2:101006800-101014800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:101007000-101025000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:101007000-101027200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr2:101007200-101011200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:101007200-101015400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:101007200-101018600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:101007200-101032000	Weak transcription	NHDF-Ad	bronchial
23	chr2:101007400-101009600	Weak transcription	Fetal Kidney	kidney
24	chr2:101007400-101010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:101007400-101011800	Weak transcription	Fetal Intestine Large	intestine
26	chr2:101007400-101014600	Strong transcription	Brain Cingulate Gyrus	brain
27	chr2:101007400-101014800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:101007400-101021600	Weak transcription	HSMMtube	muscle
29	chr2:101007600-101010400	Strong transcription	Left Ventricle	heart
30	chr2:101007600-101012800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr2:101007600-101013600	Strong transcription	Adipose Nuclei	Adipose
32	chr2:101007600-101013800	Strong transcription	Thymus	Thymus
33	chr2:101007600-101014800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:101007600-101014800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:101007600-101014800	Strong transcription	Fetal Intestine Small	intestine
36	chr2:101007600-101015000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:101007600-101015400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:101007600-101023400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:101007600-101024200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:101007600-101030600	Weak transcription	NH-A	brain
41	chr2:101007800-101009400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:101007800-101014400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:101007800-101014800	Strong transcription	Brain Anterior Caudate	brain
44	chr2:101007800-101014800	Strong transcription	Ovary	ovary
45	chr2:101007800-101015000	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:101007800-101021200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:101007800-101023800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:101007800-101024000	Weak transcription	Liver	Liver
49	chr2:101008000-101009600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:101008000-101011000	Strong transcription	Fetal Lung	lung

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