Variant report

Variant	rs1982336
Chromosome Location	chr2:98384636-98384637
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	CTCF	chr2:98384620-98384770	HCT-116	colon:	n/a	n/a
2	POLR2A	chr2:98384632-98384926	K562	blood:	n/a	n/a
3	MEF2A	chr2:98384605-98385058	GM12878	blood:	n/a	chr2:98384872-98384887 chr2:98384850-98384861 chr2:98384846-98384867 chr2:98384851-98384860 chr2:98384870-98384891 chr2:98384758-98384773 chr2:98384849-98384860 chr2:98384870-98384891 chr2:98384848-98384862 chr2:98384780-98384795 chr2:98384758-98384773 chr2:98384871-98384887
4	CTCF	chr2:98384580-98384730	NHDF-neo	bronchial:	n/a	n/a
5	MEF2C	chr2:98384530-98385043	GM12878	blood:	n/a	chr2:98384872-98384887 chr2:98384850-98384861 chr2:98384846-98384867 chr2:98384851-98384860 chr2:98384870-98384891 chr2:98384758-98384773 chr2:98384849-98384860 chr2:98384870-98384891 chr2:98384848-98384862 chr2:98384780-98384795 chr2:98384758-98384773 chr2:98384871-98384887
6	RAD21	chr2:98384620-98384899	H1-hESC	embryonic stem cell:	n/a	chr2:98384815-98384828 chr2:98384818-98384827
7	CTCF	chr2:98384620-98384770	HRPEpiC	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98326262..98327256-chr2:98384336..98384968,2	MCF-7	breast:
2	chr2:98378430..98380817-chr2:98383033..98385975,2	MCF-7	breast:

Variant related genes	Relation type
TMEM131	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10166513	0.94[ASN][1000 genomes]
rs10167772	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168543	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169155	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10175129	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10176826	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs10180434	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180837	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10183768	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184393	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10184457	0.94[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs10188497	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188713	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189414	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191101	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10192322	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10202138	0.94[ASN][1000 genomes]
rs10206684	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208070	0.82[EUR][1000 genomes]
rs10209970	0.88[ASN][1000 genomes]
rs10210520	1.00[ASN][1000 genomes]
rs10210880	0.88[ASN][1000 genomes]
rs11886417	0.88[ASN][1000 genomes]
rs11893437	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894541	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894895	1.00[ASN][1000 genomes]
rs11897301	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712117	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712120	1.00[ASN][1000 genomes]
rs12712147	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12712162	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712163	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712172	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991122	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12992955	0.94[ASN][1000 genomes]
rs13000585	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004862	0.89[ASN][1000 genomes]
rs13008678	0.81[EUR][1000 genomes]
rs13008904	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13010004	1.00[ASN][1000 genomes]
rs13012645	0.83[EUR][1000 genomes]
rs1446327	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960329	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121271	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2293679	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305142	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34190123	0.94[ASN][1000 genomes]
rs34305873	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34414288	1.00[ASN][1000 genomes]
rs34469351	0.84[ASN][1000 genomes]
rs35185431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35203092	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35402416	0.83[EUR][1000 genomes]
rs35776557	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35807655	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940587	0.88[ASN][1000 genomes]
rs36079497	0.88[ASN][1000 genomes]
rs3821053	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55753459	0.94[ASN][1000 genomes]
rs6543088	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs6543111	0.97[ASN][1000 genomes]
rs6707719	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap]
rs6707750	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6712078	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718982	0.88[ASN][1000 genomes]
rs6721323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6728312	1.00[ASN][1000 genomes]
rs6736735	0.96[CEU][hapmap]
rs6738401	0.94[ASN][1000 genomes]
rs6751727	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755021	0.94[ASN][1000 genomes]
rs6756969	0.88[ASN][1000 genomes]
rs6760008	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs68115667	0.88[ASN][1000 genomes]
rs6875	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs71429373	0.94[ASN][1000 genomes]
rs718159	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557495	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570009	1.00[ASN][1000 genomes]
rs7578638	0.88[ASN][1000 genomes]
rs7582298	0.94[ASN][1000 genomes]
rs7588227	0.88[ASN][1000 genomes]
rs7591374	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7593290	1.00[ASN][1000 genomes]
rs7594928	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595039	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599043	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605288	0.88[ASN][1000 genomes]
rs9808558	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap]
rs9973490	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1982336	INPP4A	cis	cerebellum	SCAN
rs1982336	TEKT4	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98352200-98398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:98366200-98400000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:98367200-98385000	Strong transcription	Primary B cells from peripheral blood	blood
4	chr2:98368000-98393800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:98368600-98413000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:98369600-98398800	Strong transcription	Fetal Muscle Leg	muscle
7	chr2:98369800-98384800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:98370200-98392600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:98370400-98386400	Strong transcription	Fetal Intestine Small	intestine
10	chr2:98370600-98392400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:98370600-98393800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:98370600-98407600	Weak transcription	HUVEC	blood vessel
13	chr2:98371000-98384800	Strong transcription	Fetal Intestine Large	intestine
14	chr2:98371200-98387400	Strong transcription	Liver	Liver
15	chr2:98371200-98398600	Strong transcription	Primary B cells from cord blood	blood
16	chr2:98373800-98390400	Weak transcription	K562	blood
17	chr2:98375800-98386600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:98377200-98394400	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr2:98377400-98408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:98377400-98410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:98378200-98389600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:98378600-98421400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:98379800-98385800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:98380600-98385200	Strong transcription	NHEK	skin
25	chr2:98380800-98384800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:98380800-98393800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:98381400-98397600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:98382000-98385600	Enhancers	Right Ventricle	heart
29	chr2:98382000-98388800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:98382200-98386200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:98382600-98388600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:98382600-98389600	Weak transcription	Gastric	stomach
33	chr2:98382600-98391600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:98382800-98386200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:98382800-98386200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:98382800-98386200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:98382800-98387400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:98382800-98387600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:98382800-98387600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:98382800-98387600	Weak transcription	NHDF-Ad	bronchial
41	chr2:98382800-98388400	Weak transcription	NH-A	brain
42	chr2:98382800-98389000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:98382800-98389000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:98382800-98389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:98382800-98398600	Weak transcription	Small Intestine	intestine
46	chr2:98382800-98419800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:98383000-98385400	Weak transcription	Fetal Lung	lung
48	chr2:98383000-98386400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:98383000-98386800	Enhancers	Fetal Heart	heart
50	chr2:98383000-98387400	Weak transcription	Brain Germinal Matrix	brain

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