Variant report

Variant	rs998972
Chromosome Location	chr2:187606082-187606083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187605682..187607302-chr2:187609451..187611833,2	MCF-7	breast:
2	chr2:187605948..187608819-chr2:187609356..187611446,2	K562	blood:
3	chr2:187586601..187588975-chr2:187605009..187606836,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10171481	0.85[CHB][hapmap]
rs10804007	0.85[CHB][hapmap]
rs11678190	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11683898	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11685758	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs12151442	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.87[ASN][1000 genomes]
rs12615659	1.00[CHB][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12998294	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13001028	1.00[CHB][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13006483	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs13006571	0.85[CHB][hapmap]
rs13016261	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13026081	0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13027560	0.87[ASN][1000 genomes]
rs13028817	1.00[CHB][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13030356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033579	0.81[ASN][1000 genomes]
rs1448424	1.00[CHB][hapmap]
rs17334303	0.87[ASN][1000 genomes]
rs17334422	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17406339	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17750683	0.82[EUR][1000 genomes]
rs1839123	0.87[ASN][1000 genomes]
rs1839124	0.81[ASN][1000 genomes]
rs1992898	0.85[CHB][hapmap]
rs2084448	0.87[ASN][1000 genomes]
rs2165656	0.85[CHB][hapmap]
rs2197138	0.85[CHB][hapmap]
rs2197787	0.84[CHB][hapmap]
rs2370693	0.85[CHB][hapmap]
rs2595375	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2887827	0.85[CHB][hapmap]
rs34483988	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35055112	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35251833	0.87[ASN][1000 genomes]
rs35986780	0.81[ASN][1000 genomes]
rs36117902	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768778	0.85[CHB][hapmap]
rs3768780	0.85[CHB][hapmap]
rs3816386	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs3911084	0.85[CHB][hapmap]
rs4233788	0.85[CHB][hapmap]
rs58644770	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717512	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6741369	0.85[CHB][hapmap]
rs7419327	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7589470	1.00[CHB][hapmap]
rs7593018	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7596996	0.85[CHB][hapmap]
rs9333287	0.85[CHB][hapmap]
rs9333288	0.85[CHB][hapmap]
rs9333289	1.00[CHB][hapmap]
rs9789682	0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv428069	chr2:187575692-187766209	ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs998972	FAM171B	cis	parietal	SCAN
rs998972	FAM171B	cis	cerebellum	SCAN
rs998972	STRA6	trans	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187592200-187618600	Weak transcription	Osteobl	bone
2	chr2:187596600-187611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:187596600-187626200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:187598600-187621200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:187599600-187631000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:187600000-187613200	Weak transcription	Pancreas	Pancrea
7	chr2:187600200-187611000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:187603000-187607400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:187603000-187612800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:187603200-187626400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:187603200-187626600	Weak transcription	Fetal Stomach	stomach
12	chr2:187603400-187612600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:187603400-187612800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:187603400-187613000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:187603400-187626400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:187603600-187626600	Weak transcription	Left Ventricle	heart
17	chr2:187603800-187611800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:187603800-187612800	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:187603800-187621200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:187604000-187609800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:187604000-187613200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:187604000-187618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:187604800-187613000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:187605000-187626200	Weak transcription	NHDF-Ad	bronchial
25	chr2:187605000-187626400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:187605400-187611400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:187605400-187612800	Weak transcription	Fetal Brain Female	brain
28	chr2:187605600-187608600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:187605600-187619200	Weak transcription	Ovary	ovary
30	chr2:187606000-187612800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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