Variant report

Variant	rs1035827
Chromosome Location	chr2:171920813-171920814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171910904..171913715-chr2:171918536..171922904,3	MCF-7	breast:
2	chr12:120729519..120732039-chr2:171920293..171923093,2	MCF-7	breast:
3	chr2:171920035..171922996-chr2:171924584..171926973,3	K562	blood:

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10171850	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[ASN][1000 genomes]
rs10177560	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs10182205	0.82[EUR][1000 genomes]
rs10183486	0.90[TSI][hapmap]
rs10186343	0.83[EUR][1000 genomes]
rs10191270	0.88[CEU][hapmap]
rs10198197	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10199500	0.85[CEU][hapmap]
rs10208271	0.81[EUR][1000 genomes]
rs10208341	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10210693	0.81[EUR][1000 genomes]
rs10210791	0.81[EUR][1000 genomes]
rs10210883	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1025240	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1025241	0.81[EUR][1000 genomes]
rs1035825	0.85[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs1035828	0.88[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs10803854	0.81[CEU][hapmap]
rs10803855	0.84[EUR][1000 genomes]
rs10930449	0.81[CEU][hapmap]
rs10930453	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10930455	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10930456	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10930457	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11674590	0.83[EUR][1000 genomes]
rs11696064	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11899305	0.91[EUR][1000 genomes]
rs11902369	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12053543	0.89[EUR][1000 genomes]
rs12467411	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs12473741	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs12477649	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612871	0.81[CEU][hapmap]
rs12614580	0.82[EUR][1000 genomes]
rs12618232	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618898	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12624094	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13004273	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs13008199	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs13010307	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs13025198	0.82[EUR][1000 genomes]
rs13030784	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs13034529	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs13036123	0.86[CEU][hapmap]
rs13401706	0.81[EUR][1000 genomes]
rs13402107	0.81[EUR][1000 genomes]
rs13403285	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13410683	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13411575	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13419444	0.82[EUR][1000 genomes]
rs13425247	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs13427723	0.81[EUR][1000 genomes]
rs13428613	0.81[EUR][1000 genomes]
rs13430489	0.81[EUR][1000 genomes]
rs13432813	0.81[EUR][1000 genomes]
rs1344237	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1529378	0.85[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs1529391	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs16859050	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs16859142	0.82[EUR][1000 genomes]
rs16859157	0.81[CHB][hapmap]
rs17283147	0.90[EUR][1000 genomes]
rs1863679	0.86[CHB][hapmap]
rs1962841	0.89[EUR][1000 genomes]
rs1978592	0.85[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs1989613	0.86[CHB][hapmap]
rs2010114	0.89[EUR][1000 genomes]
rs2033160	0.96[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2052808	0.90[EUR][1000 genomes]
rs2081715	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2098999	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2114595	0.90[EUR][1000 genomes]
rs2114596	0.80[EUR][1000 genomes]
rs2195117	0.81[EUR][1000 genomes]
rs2217154	0.81[EUR][1000 genomes]
rs2356423	0.80[EUR][1000 genomes]
rs2356593	0.89[EUR][1000 genomes]
rs2356597	0.90[EUR][1000 genomes]
rs2356608	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2555922	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2557794	0.85[CEU][hapmap]
rs2676131	0.96[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2676151	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs2723233	0.89[EUR][1000 genomes]
rs2723241	0.88[CEU][hapmap]
rs34518725	0.82[EUR][1000 genomes]
rs34792013	0.90[EUR][1000 genomes]
rs35173138	0.82[EUR][1000 genomes]
rs36058634	0.89[EUR][1000 genomes]
rs3731990	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731991	0.90[EUR][1000 genomes]
rs3731993	0.81[CHB][hapmap]
rs3755121	0.85[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3755124	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs3755126	0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs3770419	0.86[CHB][hapmap]
rs3770423	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs3770428	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3770433	0.85[CEU][hapmap]
rs3770438	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs4564745	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs4667673	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4668343	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4668354	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4668355	0.81[CEU][hapmap]
rs4668368	0.96[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs5028603	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs55758155	0.81[EUR][1000 genomes]
rs55996750	0.81[EUR][1000 genomes]
rs56402728	0.81[EUR][1000 genomes]
rs56405950	0.81[EUR][1000 genomes]
rs6433276	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs6711287	0.90[EUR][1000 genomes]
rs6714164	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs6716127	0.81[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs6722537	0.83[EUR][1000 genomes]
rs6730417	0.85[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6732229	0.82[EUR][1000 genomes]
rs6733178	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6734542	0.83[EUR][1000 genomes]
rs6742797	0.81[CEU][hapmap]
rs6742854	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750849	0.83[EUR][1000 genomes]
rs6754315	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6761596	0.82[EUR][1000 genomes]
rs6761642	0.85[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs731693	0.81[CEU][hapmap]
rs7421377	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754058	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580629	0.96[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs7581195	0.80[EUR][1000 genomes]
rs7582822	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs7585418	0.82[EUR][1000 genomes]
rs7593193	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7600914	0.90[EUR][1000 genomes]
rs7603316	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7603340	0.90[EUR][1000 genomes]
rs7603460	0.82[EUR][1000 genomes]
rs7606502	0.82[EUR][1000 genomes]
rs7606822	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs930035	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs930036	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs964172	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv834456	chr2:171874210-172014659	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1035827	GORASP2	cis	cerebellum	SCAN
rs1035827	DLX1	cis	cerebellum	SCAN
rs1035827	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171841600-171940000	Weak transcription	Right Ventricle	heart
2	chr2:171862800-171931200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:171878000-171943200	Weak transcription	Small Intestine	intestine
4	chr2:171878800-171940000	Weak transcription	Stomach Mucosa	stomach
5	chr2:171892400-171943400	Weak transcription	Spleen	Spleen
6	chr2:171898200-171928800	Weak transcription	Fetal Stomach	stomach
7	chr2:171898200-171946200	Weak transcription	Pancreas	Pancrea
8	chr2:171900000-171940000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:171900200-171936400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:171900200-171937800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:171900400-171975400	Weak transcription	Aorta	Aorta
12	chr2:171902000-171924200	Weak transcription	Fetal Intestine Small	intestine
13	chr2:171903000-171940000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:171904000-171921000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:171905600-171921200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:171905800-171939200	Weak transcription	HSMMtube	muscle
17	chr2:171907800-171942800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:171908200-171928400	Weak transcription	Fetal Kidney	kidney
19	chr2:171908200-171932200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:171911600-171943200	Weak transcription	NH-A	brain
21	chr2:171912400-171937400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:171914200-171925800	Weak transcription	HMEC	breast
23	chr2:171916400-171932200	Weak transcription	K562	blood
24	chr2:171916600-171924200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:171916600-171928000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:171916600-171930800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:171916600-171940000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:171916600-171944600	Weak transcription	Lung	lung
29	chr2:171916600-171950200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:171916600-171970800	Weak transcription	Ovary	ovary
31	chr2:171916800-171921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:171916800-171921800	Weak transcription	Hela-S3	cervix
33	chr2:171916800-171925600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:171916800-171926000	Weak transcription	A549	lung
35	chr2:171916800-171928800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:171916800-171935200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:171916800-171942200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:171916800-171943200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:171917000-171924200	Weak transcription	Fetal Intestine Large	intestine
40	chr2:171917000-171924400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:171917000-171925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:171917000-171925800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:171917000-171926000	Weak transcription	NHEK	skin
44	chr2:171917000-171927000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:171917000-171927400	Weak transcription	Primary T cells from cord blood	blood
46	chr2:171917000-171928400	Weak transcription	Thymus	Thymus
47	chr2:171917000-171928600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:171917000-171932000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:171917000-171934600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:171917000-171937200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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