Variant report

Variant	rs6712204
Chromosome Location	chr2:53996077-53996078
allele	A/C
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	IRF1	chr2:53995920-53996745	K562	blood:	n/a	chr2:53996450-53996462 chr2:53996120-53996134 chr2:53996036-53996050
2	POLR2A	chr2:53994401-53997166	GM18505	blood:	n/a	n/a
3	POLR2A	chr2:53994009-53996575	PBDE	blood:	n/a	n/a
4	POLR2A	chr2:53993983-53998651	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:53994075-53999332	K562	blood:	n/a	n/a
6	POLR2A	chr2:53994108-53996420	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
2	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
3	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10181752	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10181876	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10185375	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs10187718	0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10190578	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs10191950	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10193711	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197062	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200897	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10210726	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs10211188	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10211650	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10490470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11684574	0.87[ASN][1000 genomes]
rs12612589	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs12613682	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs12616124	0.90[ASN][1000 genomes]
rs12616774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12617360	0.86[ASN][1000 genomes]
rs12617668	0.91[ASN][1000 genomes]
rs12618587	0.82[ASN][1000 genomes]
rs12620190	0.90[ASN][1000 genomes]
rs12620208	0.90[ASN][1000 genomes]
rs12620325	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12621547	0.84[ASN][1000 genomes]
rs12621557	0.87[ASN][1000 genomes]
rs12621635	0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs13383167	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13393197	0.98[ASN][1000 genomes]
rs13397311	0.81[CEU][hapmap]
rs13414183	0.88[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13414472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13415842	0.87[ASN][1000 genomes]
rs13421512	0.86[ASN][1000 genomes]
rs13423576	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17045114	0.88[JPT][hapmap]
rs17045125	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs17045215	0.91[CHB][hapmap];0.95[ASN][1000 genomes]
rs17045370	0.84[GIH][hapmap]
rs17045435	0.80[GIH][hapmap]
rs2009149	0.84[ASN][1000 genomes]
rs2068017	0.87[TSI][hapmap]
rs2272249	0.81[CHD][hapmap]
rs2287344	0.91[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.90[ASN][1000 genomes]
rs2287345	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs2287512	0.81[CHD][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap]
rs2357491	0.84[CHD][hapmap]
rs28439002	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3213775	0.80[GIH][hapmap]
rs3731972	0.80[GIH][hapmap]
rs3731973	0.84[GIH][hapmap];0.84[TSI][hapmap]
rs3755120	0.82[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs3770398	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3770400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3770401	0.91[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs3821080	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3850345	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3861570	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55839073	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6545366	0.81[CEU][hapmap]
rs6705484	0.92[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs6714424	0.88[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6717642	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72793658	0.81[ASN][1000 genomes]
rs7568771	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7582542	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7586686	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595713	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs7595816	0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7609067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6712204	ASB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53994000-53996200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:53994200-53996200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:53994200-53996400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:53994200-53996400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:53994200-53996600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:53994400-53996200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr2:53994400-53996200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:53994400-53996200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:53994400-53996200	Active TSS	Fetal Stomach	stomach
10	chr2:53994400-53996400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr2:53994400-53996400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:53994800-53996200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:53995200-53996400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:53995400-53996200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr2:53995400-53996200	Flanking Active TSS	HepG2	liver
16	chr2:53995400-53996200	Flanking Active TSS	HUVEC	blood vessel
17	chr2:53995400-53996400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr2:53995400-54003600	Weak transcription	Small Intestine	intestine
19	chr2:53995600-53996200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:53995600-53996200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr2:53995600-53996200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:53995600-53996400	Enhancers	Thymus	Thymus
23	chr2:53995600-53996400	Flanking Active TSS	NHEK	skin
24	chr2:53995600-53996600	Weak transcription	Gastric	stomach
25	chr2:53995600-53996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:53995600-54005800	Weak transcription	HSMM	muscle
27	chr2:53995600-54007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:53995600-54007400	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:53995600-54007800	Weak transcription	Placenta	Placenta
30	chr2:53995600-54008400	Weak transcription	Ovary	ovary
31	chr2:53995600-54009000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:53995600-54009000	Weak transcription	Lung	lung
33	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
35	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
37	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:53995800-53996200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:53995800-53996200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:53995800-53996200	Enhancers	Primary B cells from peripheral blood	blood
41	chr2:53995800-53996200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:53995800-53996200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:53995800-53996200	Enhancers	Brain Angular Gyrus	brain
44	chr2:53995800-53996200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:53995800-53996200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:53995800-53996200	Enhancers	Stomach Mucosa	stomach
47	chr2:53995800-53996200	Flanking Active TSS	HMEC	breast
48	chr2:53995800-53996400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:53995800-53996400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:53995800-53996400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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