Variant report

Variant	rs17161569
Chromosome Location	chr7:140173102-140173103
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140170034..140173996-chr7:140176770..140179356,4	K562	blood:
2	chr7:140173004..140174685-chr7:140179512..140182205,2	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[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs10224992	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs10226064	0.96[EUR][1000 genomes]
rs10229678	0.96[EUR][1000 genomes]
rs10231547	0.96[EUR][1000 genomes]
rs10243155	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10244642	0.85[EUR][1000 genomes]
rs10256899	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10257079	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10258350	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10267810	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10269611	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]
rs10270875	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes]
rs10272040	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10272047	0.96[EUR][1000 genomes]
rs10273061	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10275127	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10275142	0.96[EUR][1000 genomes]
rs10278060	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10279172	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10280145	0.96[EUR][1000 genomes]
rs10952680	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11760895	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs11765962	0.85[EUR][1000 genomes]
rs11766079	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974068	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11978135	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12216619	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13438384	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13438583	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17161542	0.92[EUR][1000 genomes]
rs1969394	0.99[EUR][1000 genomes]
rs2001941	0.80[EUR][1000 genomes]
rs2272096	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2363824	0.97[EUR][1000 genomes]
rs2363826	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2363828	0.96[EUR][1000 genomes]
rs28412759	0.97[EUR][1000 genomes]
rs28439514	0.96[EUR][1000 genomes]
rs28538447	0.95[EUR][1000 genomes]
rs28553284	0.85[EUR][1000 genomes]
rs28563126	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28667371	0.85[EUR][1000 genomes]
rs28699169	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28784908	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28785875	0.97[EUR][1000 genomes]
rs28832645	0.96[EUR][1000 genomes]
rs2885922	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28880113	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35747234	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4385389	0.97[EUR][1000 genomes]
rs4424177	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4427086	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4431522	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs55714045	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55833852	0.96[EUR][1000 genomes]
rs55961611	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56059991	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56769703	0.96[EUR][1000 genomes]
rs58076938	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58647694	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59814044	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60137728	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61577108	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62490410	0.85[EUR][1000 genomes]
rs62490429	0.96[EUR][1000 genomes]
rs62490449	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6464773	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs6464779	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6951446	0.96[EUR][1000 genomes]
rs6962593	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs6962710	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs6963738	0.96[EUR][1000 genomes]
rs6964170	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6966049	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6966056	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6966930	0.91[EUR][1000 genomes]
rs6968931	0.95[EUR][1000 genomes]
rs6973069	0.84[EUR][1000 genomes]
rs6975307	0.96[EUR][1000 genomes]
rs7777404	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7779827	0.99[EUR][1000 genomes]
rs7784558	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7785094	0.88[CHB][hapmap];0.96[GIH][hapmap];0.81[ASN][1000 genomes]
rs7786776	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7787217	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789557	0.96[EUR][1000 genomes]
rs7790232	0.99[EUR][1000 genomes]
rs7800959	0.85[EUR][1000 genomes]
rs7805365	0.96[EUR][1000 genomes]
rs7808589	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7811669	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9648837	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9692138	0.96[EUR][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
rs17161569	JHDM1D	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr7:140151000-140173400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr7:140151800-140176600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:140155600-140175200	Weak transcription	Fetal Brain Male	brain
5	chr7:140156800-140175800	Weak transcription	Fetal Heart	heart
6	chr7:140156800-140175800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:140156800-140177400	Weak transcription	HUVEC	blood vessel
8	chr7:140156800-140177600	Weak transcription	HSMMtube	muscle
9	chr7:140156800-140178000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:140157000-140177600	Weak transcription	NH-A	brain
11	chr7:140158800-140173400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:140159400-140177400	Weak transcription	HSMM	muscle
13	chr7:140159800-140175400	Strong transcription	Fetal Intestine Small	intestine
14	chr7:140160800-140177400	Weak transcription	Osteobl	bone
15	chr7:140161000-140177000	Weak transcription	HMEC	breast
16	chr7:140161000-140177600	Weak transcription	NHDF-Ad	bronchial
17	chr7:140162200-140175800	Weak transcription	Hela-S3	cervix
18	chr7:140162400-140175800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:140165400-140176800	Weak transcription	NHLF	lung
20	chr7:140165600-140176000	Weak transcription	Stomach Mucosa	stomach
21	chr7:140165600-140177400	Weak transcription	Esophagus	oesophagus
22	chr7:140166000-140177000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:140166200-140177600	Weak transcription	Fetal Kidney	kidney
24	chr7:140167400-140177000	Weak transcription	Fetal Brain Female	brain
25	chr7:140168200-140175800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:140169400-140175800	Weak transcription	A549	lung
27	chr7:140169400-140176600	Weak transcription	NHEK	skin
28	chr7:140169400-140177000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:140169600-140177000	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:140169800-140177400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:140170000-140175800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:140170200-140175800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:140170200-140176600	Weak transcription	Ovary	ovary
34	chr7:140170400-140177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:140170800-140176400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:140170800-140178200	Weak transcription	Gastric	stomach
37	chr7:140171000-140177400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:140171200-140175400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:140171200-140176000	Weak transcription	Brain Germinal Matrix	brain
40	chr7:140171200-140176200	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:140171200-140176400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:140171200-140176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:140171200-140176600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:140171200-140176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:140171200-140176800	Weak transcription	Brain Substantia Nigra	brain
46	chr7:140171200-140177000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:140171200-140177400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:140171200-140177600	Weak transcription	Brain Anterior Caudate	brain
49	chr7:140171200-140177600	Weak transcription	Psoas Muscle	Psoas
50	chr7:140171400-140175800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links