Variant report

Variant	rs2147950
Chromosome Location	chr1:84465545-84465546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:84463776-84465932	H1-neurons	neurons:	n/a	chr1:84464459-84464479 chr1:84465417-84465426
2	JUND	chr1:84463790-84465797	SK-N-SH	brain:	n/a	chr1:84465068-84465077 chr1:84464109-84464117 chr1:84464107-84464119 chr1:84464316-84464325 chr1:84464107-84464114
3	CHD1	chr1:84464441-84465805	IMR90	lung:	n/a	n/a
4	HA-E2F1	chr1:84464499-84465574	MCF-7	breast:	n/a	n/a
5	GATA2	chr1:84464471-84465715	SH-SY5Y	brain:	n/a	n/a
6	TBL1XR1	chr1:84465539-84465669	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84464994..84466919-chr1:84468968..84470510,3	K562	blood:
2	chr1:84463410..84466364-chr1:84542152..84546505,5	K562	blood:
3	chr1:84464864..84467059-chr1:84542152..84543740,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTLL7-1	chr1:84464970-84465750	XLOC_000888

Variant related genes	Relation type
TTLL7	TF binding region
ENSG00000142875	Chromatin interaction
ENSG00000271576	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10127737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10465746	0.93[ASN][1000 genomes]
rs10493741	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10493744	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10874423	0.90[ASN][1000 genomes]
rs10874424	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11163861	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11163862	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs11163865	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs11163866	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs11163867	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs11163868	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11163872	0.85[ASN][1000 genomes]
rs11163874	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163875	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163876	0.94[ASN][1000 genomes]
rs11163877	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11163878	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163879	0.97[ASN][1000 genomes]
rs11163884	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11163885	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11163886	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11163887	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807807	0.94[ASN][1000 genomes]
rs12070578	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12118434	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12119275	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12121175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127266	0.88[ASN][1000 genomes]
rs12133778	0.88[ASN][1000 genomes]
rs12135028	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12139191	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs12140068	0.93[ASN][1000 genomes]
rs12141272	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs12145258	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs12145516	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12146038	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12184292	0.84[ASN][1000 genomes]
rs12401314	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12402130	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12406984	0.92[ASN][1000 genomes]
rs12407641	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12410398	0.96[ASN][1000 genomes]
rs12410617	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12723239	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12730621	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12732697	0.83[ASN][1000 genomes]
rs12738214	0.84[ASN][1000 genomes]
rs12748268	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12749350	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12757632	0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs12758441	0.83[ASN][1000 genomes]
rs12759527	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1324484	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1324486	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs1359331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1475263	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1536165	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1536166	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1570690	0.90[ASN][1000 genomes]
rs1570691	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs1602999	0.90[EUR][1000 genomes]
rs17099118	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17475760	0.95[ASN][1000 genomes]
rs17534614	0.91[ASN][1000 genomes]
rs1871924	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs1871925	0.99[ASN][1000 genomes]
rs1886769	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886770	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925710	0.95[ASN][1000 genomes]
rs1952065	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1952066	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2024591	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2147392	0.91[ASN][1000 genomes]
rs2224990	0.98[ASN][1000 genomes]
rs2389616	0.96[ASN][1000 genomes]
rs2389617	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2389647	0.91[ASN][1000 genomes]
rs2389648	0.92[ASN][1000 genomes]
rs2389649	0.91[ASN][1000 genomes]
rs2477201	0.85[JPT][hapmap]
rs28445286	0.96[ASN][1000 genomes]
rs28567085	0.98[ASN][1000 genomes]
rs28726372	0.81[ASN][1000 genomes]
rs34155960	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34274953	0.87[ASN][1000 genomes]
rs34636124	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35485748	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35946036	0.98[ASN][1000 genomes]
rs35969331	0.98[ASN][1000 genomes]
rs4258241	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4907186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4907188	0.84[ASN][1000 genomes]
rs4907189	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4907190	0.96[ASN][1000 genomes]
rs4907191	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs558567	0.85[JPT][hapmap]
rs575633	0.85[JPT][hapmap]
rs598531	0.85[JPT][hapmap]
rs639666	0.85[JPT][hapmap]
rs663136	0.85[JPT][hapmap]
rs6658559	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6663949	0.82[AFR][1000 genomes]
rs6667468	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670658	0.98[ASN][1000 genomes]
rs6685344	0.86[ASN][1000 genomes]
rs6687372	0.98[ASN][1000 genomes]
rs6692233	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6694752	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6699501	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs670284	0.85[JPT][hapmap]
rs6703382	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6703493	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs685472	0.85[JPT][hapmap]
rs686839	0.85[JPT][hapmap]
rs7531537	0.96[ASN][1000 genomes]
rs7550413	0.80[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7551787	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs882897	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs936661	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs942848	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs942849	0.98[ASN][1000 genomes]
rs9660265	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs980417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs980418	0.89[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2147950	LPHN2	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84460000-84465600	Active TSS	Brain Anterior Caudate	brain
2	chr1:84461200-84465600	Active TSS	Brain Cingulate Gyrus	brain
3	chr1:84461800-84465600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr1:84461800-84465800	Active TSS	Aorta	Aorta
5	chr1:84461800-84465800	Active TSS	Brain Substantia Nigra	brain
6	chr1:84462000-84465600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:84462000-84466000	Active TSS	Brain Hippocampus Middle	brain
8	chr1:84462000-84467000	Active TSS	Brain Angular Gyrus	brain
9	chr1:84463000-84465800	Active TSS	NHLF	lung
10	chr1:84463400-84465600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:84463600-84466400	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:84463800-84465600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:84463800-84465600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr1:84463800-84465600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:84463800-84465600	Active TSS	Right Atrium	heart
16	chr1:84463800-84465600	Active TSS	Right Ventricle	heart
17	chr1:84463800-84465800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:84463800-84465800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:84464000-84465600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:84464000-84465600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:84464000-84465600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:84464000-84465600	Active TSS	Hela-S3	cervix
23	chr1:84464000-84465600	Active TSS	K562	blood
24	chr1:84464200-84465600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr1:84464200-84465600	Active TSS	Fetal Stomach	stomach
26	chr1:84464200-84465600	Active TSS	Ovary	ovary
27	chr1:84464200-84465800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:84464200-84465800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:84464400-84465600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:84464400-84465600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:84464400-84465600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
32	chr1:84464600-84465600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:84464600-84465600	Active TSS	Fetal Brain Male	brain
34	chr1:84464600-84466000	Active TSS	Brain Germinal Matrix	brain
35	chr1:84464800-84465600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:84465000-84465600	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:84465000-84465600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:84465000-84465600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:84465000-84465600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:84465000-84465800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:84465200-84465600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:84465200-84465600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr1:84465200-84465600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
44	chr1:84465200-84465600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr1:84465200-84465600	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
46	chr1:84465200-84465600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
47	chr1:84465200-84465600	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:84465200-84465600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
49	chr1:84465200-84465600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:84465200-84465600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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