Variant report

Variant	rs3752431
Chromosome Location	chr2:231280223-231280224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:231280216-231281274	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:231280192-231281486	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:231279849-231281725	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:231279532-231281659	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:231280079-231281461	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:231279555-231281531	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:231279589-231281563	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:231279542-231281558	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231191400..231192273-chr2:231280039..231281003,2	MCF-7	breast:

Variant related genes	Relation type
SP100	TF binding region
ENSG00000185404	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1074886	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11675127	0.87[ASN][1000 genomes]
rs11675135	0.87[ASN][1000 genomes]
rs11676089	0.87[ASN][1000 genomes]
rs11676310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677646	0.85[ASN][1000 genomes]
rs11679026	0.85[ASN][1000 genomes]
rs11681234	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11681358	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11687964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688362	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11688458	0.86[ASN][1000 genomes]
rs11692506	1.00[JPT][hapmap]
rs11692527	0.87[ASN][1000 genomes]
rs11692602	0.87[ASN][1000 genomes]
rs11693767	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11694346	0.93[ASN][1000 genomes]
rs11694422	0.89[ASN][1000 genomes]
rs11694428	0.89[ASN][1000 genomes]
rs11695277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12694865	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1427284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17273079	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17332171	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17332742	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs17333189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2303608	0.93[ASN][1000 genomes]
rs35919859	0.89[ASN][1000 genomes]
rs3754940	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754941	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs3754942	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754943	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769849	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3815885	0.93[ASN][1000 genomes]
rs3893836	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55637456	0.87[ASN][1000 genomes]
rs55770359	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55893188	0.85[ASN][1000 genomes]
rs55964110	0.87[ASN][1000 genomes]
rs56007282	0.93[ASN][1000 genomes]
rs56044062	0.87[ASN][1000 genomes]
rs56052963	0.87[ASN][1000 genomes]
rs56105857	0.87[ASN][1000 genomes]
rs56108366	0.87[ASN][1000 genomes]
rs56251216	0.87[ASN][1000 genomes]
rs56303947	0.87[ASN][1000 genomes]
rs56372741	0.87[ASN][1000 genomes]
rs56401027	0.85[ASN][1000 genomes]
rs6436933	0.87[ASN][1000 genomes]
rs6706167	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6713447	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6713465	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6722656	0.90[ASN][1000 genomes]
rs6725726	0.90[ASN][1000 genomes]
rs6732684	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6732940	0.87[ASN][1000 genomes]
rs6748339	0.87[ASN][1000 genomes]
rs6748445	0.87[ASN][1000 genomes]
rs6750712	0.93[ASN][1000 genomes]
rs6753500	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6759292	0.93[ASN][1000 genomes]
rs6761255	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs68096532	0.93[ASN][1000 genomes]
rs72495174	0.87[ASN][1000 genomes]
rs72495175	0.87[ASN][1000 genomes]
rs72495176	0.87[ASN][1000 genomes]
rs72495180	0.87[ASN][1000 genomes]
rs72495181	0.87[ASN][1000 genomes]
rs72495182	0.87[ASN][1000 genomes]
rs72495183	0.93[ASN][1000 genomes]
rs72495185	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs725202	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs72994332	0.85[ASN][1000 genomes]
rs72996270	0.85[ASN][1000 genomes]
rs72996292	0.87[ASN][1000 genomes]
rs72998203	0.87[ASN][1000 genomes]
rs72998264	0.93[ASN][1000 genomes]
rs72998283	0.93[ASN][1000 genomes]
rs73000239	0.93[ASN][1000 genomes]
rs73000253	0.93[ASN][1000 genomes]
rs73000268	0.93[ASN][1000 genomes]
rs7559665	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7563909	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7568128	0.93[ASN][1000 genomes]
rs7585646	0.87[ASN][1000 genomes]
rs7585731	0.87[ASN][1000 genomes]
rs7589948	0.87[ASN][1000 genomes]
rs7597033	0.87[ASN][1000 genomes]
rs7606804	0.93[ASN][1000 genomes]
rs999888	1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3752431	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231277200-231280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:231277200-231280400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:231277200-231280400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:231277200-231280400	Weak transcription	Aorta	Aorta
5	chr2:231277200-231280400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:231277200-231280400	Weak transcription	Psoas Muscle	Psoas
7	chr2:231277200-231280400	Weak transcription	Small Intestine	intestine
8	chr2:231277200-231280400	Weak transcription	HSMM	muscle
9	chr2:231277200-231280400	Weak transcription	HSMMtube	muscle
10	chr2:231277200-231280400	Weak transcription	NH-A	brain
11	chr2:231277200-231280800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:231277400-231280400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:231277400-231280400	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:231277400-231280400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr2:231277400-231280400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:231277400-231280400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:231277400-231280400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:231277400-231280400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:231277400-231280400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:231277400-231280400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr2:231277400-231280400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:231277400-231280400	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:231277400-231280400	Weak transcription	Fetal Lung	lung
24	chr2:231277400-231280400	Weak transcription	A549	lung
25	chr2:231277400-231280400	Enhancers	HepG2	liver
26	chr2:231277400-231280600	Weak transcription	Fetal Brain Male	brain
27	chr2:231277400-231280600	Weak transcription	Fetal Kidney	kidney
28	chr2:231277600-231280400	Enhancers	Primary B cells from cord blood	blood
29	chr2:231277600-231280400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:231277600-231280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:231277600-231280400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:231277600-231280400	Weak transcription	Thymus	Thymus
33	chr2:231277600-231280400	Weak transcription	NHLF	lung
34	chr2:231277600-231280600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:231277800-231280400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:231277800-231280400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:231277800-231280600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:231277800-231280600	Weak transcription	Brain Anterior Caudate	brain
39	chr2:231278000-231280400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:231278000-231280400	Weak transcription	Left Ventricle	heart
41	chr2:231278200-231280400	Weak transcription	Fetal Heart	heart
42	chr2:231278200-231280400	Weak transcription	K562	blood
43	chr2:231278200-231280400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:231278400-231280400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:231278400-231280400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:231278600-231280400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:231278600-231280400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:231278600-231280400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:231278600-231280400	Enhancers	Fetal Thymus	thymus
50	chr2:231278600-231280400	Enhancers	NHEK	skin

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