Variant report

Variant	rs10269611
Chromosome Location	chr7:140151648-140151649
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140149903..140153274-chr7:140154077..140157814,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133606	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10216203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10224992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10226064	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10229678	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10231547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10243155	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10244642	0.87[EUR][1000 genomes]
rs10256899	0.96[EUR][1000 genomes]
rs10257079	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10258350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10267810	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10270875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10272040	0.97[EUR][1000 genomes]
rs10272047	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10273061	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10275127	0.99[EUR][1000 genomes]
rs10275142	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10278060	0.85[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10279172	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10280145	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10952680	0.91[EUR][1000 genomes]
rs11760895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11765962	0.87[EUR][1000 genomes]
rs11766079	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11974068	0.96[EUR][1000 genomes]
rs11978135	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes]
rs12216619	0.99[EUR][1000 genomes]
rs13438384	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13438583	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17161542	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17161569	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1969394	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2001941	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[EUR][1000 genomes]
rs2272096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2363824	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2363826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2363828	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28412759	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28439514	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28538447	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28553284	0.87[EUR][1000 genomes]
rs28563126	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28667371	0.87[EUR][1000 genomes]
rs28699169	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28784908	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28785875	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28832645	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2885922	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28880113	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35747234	0.99[EUR][1000 genomes]
rs4385389	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4424177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4427086	0.95[EUR][1000 genomes]
rs4431522	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55714045	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55833852	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55961611	0.99[EUR][1000 genomes]
rs56059991	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56769703	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58076938	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58647694	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59814044	0.96[EUR][1000 genomes]
rs60137728	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61577108	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62490410	0.87[EUR][1000 genomes]
rs62490429	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62490449	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6464773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6464779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6951446	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6962593	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6962710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6963738	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6964170	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6966056	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6966930	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6968931	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6973069	0.85[EUR][1000 genomes]
rs6975307	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7777404	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779827	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7784558	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7785094	0.96[GIH][hapmap]
rs7786776	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7787217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789557	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7790232	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7800959	0.87[EUR][1000 genomes]
rs7805365	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7808589	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811669	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648837	0.99[EUR][1000 genomes]
rs9692138	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464734	chr7:140108096-140217670	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv608500	chr7:140108096-140217670	Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1803443	chr7:140146694-140263109	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10269611	JHDM1D	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140126400-140176600	Weak transcription	Right Atrium	heart
2	chr7:140133200-140154200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:140135800-140156000	Weak transcription	NHEK	skin
4	chr7:140136600-140154600	Weak transcription	Fetal Brain Male	brain
5	chr7:140139400-140152400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:140140800-140153800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:140142000-140154200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:140144000-140152600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:140144000-140152800	Weak transcription	Ovary	ovary
10	chr7:140144000-140153200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:140144000-140153800	Weak transcription	HepG2	liver
12	chr7:140144000-140154200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:140144000-140154200	Weak transcription	A549	lung
14	chr7:140144000-140154400	Weak transcription	Pancreas	Pancrea
15	chr7:140144200-140152600	Weak transcription	K562	blood
16	chr7:140144800-140153600	Weak transcription	Brain Germinal Matrix	brain
17	chr7:140145200-140152000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr7:140145200-140152600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:140145800-140152800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:140146000-140153800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:140146400-140154400	Weak transcription	HMEC	breast
22	chr7:140146600-140153400	Weak transcription	Gastric	stomach
23	chr7:140146800-140153400	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:140146800-140154400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:140147200-140153000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:140147400-140153600	Weak transcription	NH-A	brain
27	chr7:140147400-140153800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:140147600-140151800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:140147600-140152600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:140147600-140154600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:140147800-140153600	Weak transcription	Fetal Lung	lung
32	chr7:140147800-140154000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr7:140148000-140152200	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:140148000-140152400	Weak transcription	Dnd41	blood
35	chr7:140148000-140152800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:140148000-140153200	Weak transcription	Fetal Kidney	kidney
37	chr7:140148000-140153600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr7:140148200-140153600	Weak transcription	Brain Substantia Nigra	brain
39	chr7:140148400-140152200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:140149000-140151800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr7:140149000-140152200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:140149000-140152400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr7:140149200-140151800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:140149200-140151800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr7:140149400-140151800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:140149400-140152600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:140149400-140152600	Weak transcription	NHDF-Ad	bronchial
48	chr7:140149600-140152200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:140149600-140152400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:140149600-140152600	Weak transcription	Spleen	Spleen

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