Variant report

Variant	rs6704644
Chromosome Location	chr2:234406655-234406656
allele	G/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	chr2:234406272-234406889	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234404504..234406876-chr2:234739242..234740869,2	MCF-7	breast:
2	chr2:234405752..234408399-chr2:234409710..234413994,3	K562	blood:
3	chr2:234406540..234408040-chr2:234435707..234437772,2	K562	blood:

Variant related genes	Relation type
USP40	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1046976	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10929178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11675254	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11675858	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11676524	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11686188	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11694406	1.00[CHB][hapmap]
rs3754595	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3796090	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs3796092	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3820744	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs3828307	1.00[CHB][hapmap]
rs4047189	0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6746234	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753242	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs72980392	0.90[AFR][1000 genomes]
rs72980395	0.86[EUR][1000 genomes]
rs72980402	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72982309	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982316	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982325	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587876	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs7598771	1.00[CHB][hapmap]

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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bilirubin levels	21646302	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6704644	ECEL1P2	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
5	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
7	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
9	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
11	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
12	chr2:234395800-234408000	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:234395800-234411400	Strong transcription	Liver	Liver
14	chr2:234396000-234407000	Strong transcription	HepG2	liver
15	chr2:234396400-234407600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr2:234396800-234409600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:234397800-234411400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
19	chr2:234398200-234411200	Weak transcription	Esophagus	oesophagus
20	chr2:234398200-234411200	Weak transcription	Thymus	Thymus
21	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
22	chr2:234398600-234408800	Weak transcription	NH-A	brain
23	chr2:234398600-234431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:234398800-234407600	Strong transcription	HSMM	muscle
25	chr2:234398800-234408800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:234399000-234408400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:234399000-234408400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:234399000-234409000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:234399000-234409200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:234399600-234410000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:234400200-234410600	Weak transcription	Small Intestine	intestine
32	chr2:234400400-234430000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:234401200-234407200	Weak transcription	Fetal Lung	lung
34	chr2:234401200-234410400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:234401200-234411200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:234401200-234430800	Weak transcription	NHLF	lung
37	chr2:234401800-234410400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:234402200-234409800	Weak transcription	Brain Substantia Nigra	brain
39	chr2:234402200-234409800	Weak transcription	NHDF-Ad	bronchial
40	chr2:234402200-234410600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:234402200-234411200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:234402200-234411200	Weak transcription	Pancreas	Pancrea
43	chr2:234402200-234411200	Weak transcription	Spleen	Spleen
44	chr2:234402200-234411200	Weak transcription	Dnd41	blood
45	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
46	chr2:234402600-234410000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:234402600-234410400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:234402600-234429800	Weak transcription	Right Ventricle	heart
49	chr2:234402600-234430600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:234402600-234436800	Weak transcription	Gastric	stomach

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