Variant report

Variant	rs7529690
Chromosome Location	chr1:225714770-225714771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225710717..225715059-chr1:225715137..225718400,6	K562	blood:
2	chr1:225712577..225715165-chr1:225716923..225719442,2	MCF-7	breast:
3	chr1:225713990..225716472-chr1:225723399..225725793,2	K562	blood:
4	chr1:225712005..225714955-chr1:225715137..225718400,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10495242	0.87[YRI][hapmap]
rs10799312	0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs10799320	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915836	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11588279	0.83[CHB][hapmap]
rs12032961	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12034829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1340865	0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs1771316	0.93[YRI][hapmap]
rs1891000	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[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2039620	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066233	0.83[CHB][hapmap]
rs3766930	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs3893032	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs4233220	0.82[ASN][1000 genomes]
rs4554690	0.87[ASN][1000 genomes]
rs4653638	0.87[JPT][hapmap]
rs481746	0.82[AMR][1000 genomes]
rs499782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426075	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6692054	0.82[ASN][1000 genomes]
rs6696038	0.83[CHB][hapmap]
rs6702641	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7522622	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7527014	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7527184	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9426126	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9725758	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7529690	C1orf95	cis	cerebellum	SCAN
rs7529690	DUSP10	cis	parietal	SCAN
rs7529690	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
3	chr1:225697200-225716600	Weak transcription	Right Atrium	heart
4	chr1:225697400-225715400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:225698600-225721000	Weak transcription	Small Intestine	intestine
7	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:225700000-225726400	Weak transcription	HMEC	breast
9	chr1:225701400-225727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
11	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
12	chr1:225704200-225721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:225705600-225715800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:225705600-225717600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:225705800-225716000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:225705800-225716800	Weak transcription	HepG2	liver
18	chr1:225705800-225717000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:225705800-225717400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225705800-225717400	Weak transcription	Esophagus	oesophagus
21	chr1:225705800-225718800	Weak transcription	Lung	lung
22	chr1:225705800-225726600	Weak transcription	NHEK	skin
23	chr1:225707000-225717400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:225707200-225715400	Weak transcription	Pancreas	Pancrea
25	chr1:225707200-225716600	Weak transcription	Fetal Stomach	stomach
26	chr1:225707200-225717600	Weak transcription	Aorta	Aorta
27	chr1:225707200-225726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:225707200-225755000	Weak transcription	Gastric	stomach
29	chr1:225707400-225715400	Weak transcription	NH-A	brain
30	chr1:225707400-225716600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:225707400-225716600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:225707400-225717000	Weak transcription	NHLF	lung
33	chr1:225707400-225726600	Weak transcription	Brain Angular Gyrus	brain
34	chr1:225707600-225715600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:225707600-225716000	Weak transcription	HSMM	muscle
36	chr1:225707600-225716600	Weak transcription	NHDF-Ad	bronchial
37	chr1:225707600-225716800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:225709000-225721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:225709200-225720000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:225711000-225718800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:225711200-225716000	Weak transcription	Stomach Mucosa	stomach
42	chr1:225711200-225718800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:225711400-225726600	Weak transcription	Fetal Brain Female	brain
44	chr1:225711600-225716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:225711600-225716000	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:225711600-225720600	Weak transcription	Fetal Intestine Small	intestine
47	chr1:225711600-225720600	Weak transcription	HSMMtube	muscle
48	chr1:225711600-225721200	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:225712200-225715400	Weak transcription	Fetal Brain Male	brain
50	chr1:225712200-225715600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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