Variant report

Variant	rs1895694
Chromosome Location	chr2:148619746-148619747
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	chr2:148618900..148620557-chr2:148620956..148623772,2	MCF-7	breast:
2	chr2:148599271..148602254-chr2:148619088..148621822,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121989	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10180655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11686483	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12105745	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1227304	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1234416	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12622150	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12989087	0.96[ASN][1000 genomes]
rs13016400	0.81[CEU][hapmap]
rs13016893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13430086	0.89[CEU][hapmap];0.91[ASN][1000 genomes]
rs2042555	0.80[EUR][1000 genomes]
rs2113792	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2113794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2194695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603597	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2603600	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627019	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2627025	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3768684	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs3768686	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs3768688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820716	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4419186	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55816333	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56073268	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709182	0.96[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs6713811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.97[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];0.98[ASN][1000 genomes]
rs6731371	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7566230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7582403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7593570	0.86[ASN][1000 genomes]
rs9287411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1895694	ACVR2A	cis	parietal	SCAN
rs1895694	MMADHC	cis	parietal	SCAN
rs1895694	ORC4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148604000-148620000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:148606000-148620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
4	chr2:148606200-148620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:148609400-148620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:148613000-148627400	Weak transcription	Pancreas	Pancrea
7	chr2:148613000-148640800	Weak transcription	Lung	lung
8	chr2:148613200-148619800	Weak transcription	Fetal Intestine Large	intestine
9	chr2:148613200-148625600	Weak transcription	Right Atrium	heart
10	chr2:148613200-148631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:148614400-148620400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:148614600-148621400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:148615400-148623200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:148615800-148621000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:148615800-148626200	Weak transcription	Ovary	ovary
16	chr2:148616200-148621000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:148616400-148619800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr2:148616600-148620400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:148616800-148636200	Weak transcription	Small Intestine	intestine
20	chr2:148617600-148620600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:148617800-148621400	Weak transcription	HUVEC	blood vessel
22	chr2:148617800-148624400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:148618000-148620000	Weak transcription	Psoas Muscle	Psoas
24	chr2:148618000-148620600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:148618000-148620800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:148618000-148621600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:148618000-148625400	Weak transcription	Right Ventricle	heart
28	chr2:148618000-148625600	Weak transcription	HSMMtube	muscle
29	chr2:148618000-148627400	Weak transcription	Fetal Brain Male	brain
30	chr2:148618000-148627400	Weak transcription	Gastric	stomach
31	chr2:148618200-148620000	Weak transcription	Brain Germinal Matrix	brain
32	chr2:148618400-148620400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:148618400-148620400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:148618400-148620600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:148618400-148620600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:148618400-148620800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:148618400-148626800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:148618400-148627400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:148618600-148626800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:148618600-148627000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:148619000-148621000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:148619200-148620200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:148619200-148620800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr2:148619200-148621000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr2:148619200-148621000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:148619200-148621200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:148619200-148621400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:148619200-148621800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:148619400-148619800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:148619400-148620000	Enhancers	Duodenum Mucosa	Duodenum

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