Variant report

Variant	rs4424177
Chromosome Location	chr7:140167511-140167512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140096348..140098291-chr7:140167176..140170058,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157800	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10216203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10224992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10226064	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10229678	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10231547	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10243155	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10244642	0.84[EUR][1000 genomes]
rs10256899	0.93[EUR][1000 genomes]
rs10257079	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10258350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267810	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10269611	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]
rs10270875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10272040	0.95[EUR][1000 genomes]
rs10272047	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10273061	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275127	0.96[EUR][1000 genomes]
rs10275142	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10278060	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10279172	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10280145	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10952680	0.93[EUR][1000 genomes]
rs11760895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765962	0.84[EUR][1000 genomes]
rs11766079	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11974068	0.93[EUR][1000 genomes]
rs11978135	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs12216619	0.96[EUR][1000 genomes]
rs13438384	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161542	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17161569	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1969394	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2001941	0.90[CHB][hapmap]
rs2272096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2363824	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2363828	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28412759	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28439514	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28538447	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28553284	0.84[EUR][1000 genomes]
rs28563126	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28667371	0.84[EUR][1000 genomes]
rs28699169	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28784908	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28785875	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28832645	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2885922	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28880113	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35747234	0.96[EUR][1000 genomes]
rs4385389	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4427086	0.97[EUR][1000 genomes]
rs4431522	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55714045	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833852	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55961611	0.96[EUR][1000 genomes]
rs56059991	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56769703	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58076938	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58647694	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59356360	0.85[AFR][1000 genomes]
rs59814044	0.93[EUR][1000 genomes]
rs60137728	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61577108	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62490410	0.84[EUR][1000 genomes]
rs62490429	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62490449	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6464773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6464779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951446	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6962593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6962710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6963738	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6964170	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966056	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966930	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6968931	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6973069	0.83[EUR][1000 genomes]
rs6975307	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7777404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779827	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7784558	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7785094	0.96[GIH][hapmap]
rs7786776	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789557	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7790232	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7800959	0.84[EUR][1000 genomes]
rs7805365	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808589	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7811669	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9648837	0.96[EUR][1000 genomes]
rs9692138	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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
rs4424177	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	chr7:140150800-140171800	Strong transcription	Fetal Thymus	thymus
3	chr7:140151000-140171600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:140151000-140171600	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:140151000-140173400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:140151200-140171600	Strong transcription	Adipose Nuclei	Adipose
7	chr7:140151200-140172200	Strong transcription	Fetal Stomach	stomach
8	chr7:140151400-140171800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr7:140151400-140172200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:140151600-140172200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:140151800-140172200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:140151800-140176600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:140152200-140171400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:140152200-140172000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:140152200-140172000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr7:140152200-140172000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:140152200-140172200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr7:140152400-140171600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:140152400-140171600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr7:140152400-140171800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:140152400-140172200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:140152600-140171800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:140152600-140171800	Strong transcription	K562	blood
24	chr7:140152600-140172200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:140152800-140171600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:140153200-140167600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:140153200-140171800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:140153800-140172200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr7:140155600-140175200	Weak transcription	Fetal Brain Male	brain
30	chr7:140156600-140169200	Weak transcription	Small Intestine	intestine
31	chr7:140156600-140171400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:140156800-140167600	Weak transcription	Brain Substantia Nigra	brain
33	chr7:140156800-140172600	Strong transcription	Fetal Intestine Large	intestine
34	chr7:140156800-140175800	Weak transcription	Fetal Heart	heart
35	chr7:140156800-140175800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:140156800-140177400	Weak transcription	HUVEC	blood vessel
37	chr7:140156800-140177600	Weak transcription	HSMMtube	muscle
38	chr7:140156800-140178000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:140157000-140177600	Weak transcription	NH-A	brain
40	chr7:140157400-140171600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:140157400-140172000	Strong transcription	Liver	Liver
42	chr7:140157400-140172000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr7:140158400-140172000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:140158800-140172000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:140158800-140173400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:140159000-140169200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:140159000-140171200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:140159000-140171600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr7:140159000-140172000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:140159200-140170600	Weak transcription	Psoas Muscle	Psoas

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