Variant report

Variant	rs3905328
Chromosome Location	chr1:169351596-169351597
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	chr1:169345044..169346763-chr1:169350372..169352525,2	MCF-7	breast:
2	chr1:169346482..169351680-chr1:169353078..169360345,13	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1018831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs10737546	0.81[YRI][hapmap]
rs10753786	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10800424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10800425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10800435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs10800438	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800440	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800441	0.85[CEU][hapmap]
rs10800447	0.81[YRI][hapmap]
rs10919120	0.88[CHD][hapmap]
rs10919124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919132	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10919168	0.81[ASN][1000 genomes]
rs10919174	0.82[JPT][hapmap]
rs1124843	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs12024897	0.85[CEU][hapmap]
rs12029566	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1208370	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1208377	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs12563090	0.85[CEU][hapmap]
rs1400836	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs1517747	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1591733	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap]
rs1856303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1914505	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980198	0.85[CEU][hapmap]
rs1983546	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2003653	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2138898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176474	0.82[AMR][1000 genomes]
rs2275299	0.85[CEU][hapmap]
rs2300158	0.89[YRI][hapmap]
rs3766095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3818844	0.85[CEU][hapmap]
rs3820059	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4656183	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656670	0.85[CEU][hapmap]
rs4656672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427185	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[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs6427187	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656822	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap]
rs6669741	0.85[CEU][hapmap]
rs6669901	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672589	0.81[YRI][hapmap]
rs6677410	0.85[CEU][hapmap]
rs6696810	0.85[CEU][hapmap]
rs6700375	0.81[ASN][1000 genomes]
rs7415756	0.88[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521582	1.00[CHD][hapmap]
rs7533257	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap]
rs7534737	0.85[CEU][hapmap]
rs7535765	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539415	0.85[CEU][hapmap]
rs7544221	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3905328	KIFAP3	cis	cerebellum	SCAN
rs3905328	NME7	cis	Thyroid	GTEx
rs3905328	NME7	cis	Artery Tibial	GTEx
rs3905328	C1orf114	cis	cerebellum	SCAN
rs3905328	SELP	cis	cerebellum	SCAN
rs3905328	NME7	cis	Esophagus Muscularis	GTEx
rs3905328	C1orf114	cis	parietal	SCAN
rs3905328	NME7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
2	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
3	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
4	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:169338000-169365200	Weak transcription	Gastric	stomach
6	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
7	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
13	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
17	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
18	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
19	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:169339200-169351800	Weak transcription	Fetal Brain Male	brain
22	chr1:169340200-169356400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:169340400-169366000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:169344200-169360200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:169344800-169359200	Strong transcription	HSMM	muscle
27	chr1:169344800-169361200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr1:169344800-169362600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr1:169344800-169365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:169345000-169355400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:169345000-169360800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:169345000-169366000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:169345200-169352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:169345200-169352400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:169345200-169353600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:169345400-169353600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:169345400-169354000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:169345400-169366000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:169345600-169352400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:169345600-169352800	Strong transcription	HUVEC	blood vessel
41	chr1:169345600-169355000	Strong transcription	A549	lung
42	chr1:169345600-169360800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:169345600-169366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:169345800-169354200	Strong transcription	NHDF-Ad	bronchial
45	chr1:169345800-169360800	Strong transcription	NH-A	brain
46	chr1:169345800-169365000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:169345800-169365400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:169345800-169366000	Strong transcription	Placenta	Placenta
49	chr1:169345800-169366400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:169346600-169354800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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