Variant report

Variant	rs12538787
Chromosome Location	chr7:129499232-129499233
allele	A/G
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	NFIC	chr7:129498974-129499481	GM12878	blood:	n/a	n/a
2	SPI1	chr7:129499074-129499341	GM12891	blood:	n/a	n/a
3	STAT3	chr7:129499136-129499336	MCF10A-Er-Src	breast:	n/a	n/a
4	SPI1	chr7:129498920-129499435	HL-60	blood:	n/a	n/a
5	NFIC	chr7:129498995-129499544	GM12878	blood:	n/a	n/a
6	MTA3	chr7:129499006-129499453	GM12878	blood:	n/a	n/a
7	BCLAF1	chr7:129499018-129499454	GM12878	blood:	n/a	n/a
8	RUNX3	chr7:129499031-129499493	GM12878	blood:	n/a	chr7:129499278-129499287 chr7:129499278-129499287
9	RUNX3	chr7:129498981-129499556	GM12878	blood:	n/a	chr7:129499278-129499287 chr7:129499278-129499287
10	CCNT2	chr7:129499155-129499355	K562	blood:	n/a	n/a
11	MEF2A	chr7:129498991-129499417	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr7:129499168-129499438	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:129498900-129499881	SK-N-SH	brain:	n/a	n/a
14	IKZF1	chr7:129499026-129499646	GM12878	blood:	n/a	chr7:129499131-129499139

Variant related genes	Relation type
UBE2H	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12530557	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531622	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531936	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532612	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533290	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533464	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12533528	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533953	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12534043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534061	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535347	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535857	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12536424	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537150	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537604	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537782	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539145	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539653	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539800	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540479	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540517	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464970	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464971	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464972	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1471874	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471877	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559301	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965567	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1965568	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631601	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2727457	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34930431	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35189138	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55675451	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732825	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55735840	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55748031	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55767113	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55769831	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772531	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798026	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55809128	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56022754	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025626	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56034137	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56080853	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085705	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56094908	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56117230	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153730	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167610	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56176516	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56191413	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321762	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332361	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333543	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56376893	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56381627	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56408895	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129475000-129534800	Weak transcription	Colonic Mucosa	Colon
2	chr7:129479400-129543600	Weak transcription	Thymus	Thymus
3	chr7:129481400-129499800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:129481400-129510000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:129484200-129503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:129485400-129503800	Weak transcription	Lung	lung
7	chr7:129485600-129502400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:129486400-129502400	Weak transcription	Esophagus	oesophagus
9	chr7:129486400-129505400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:129486600-129501400	Weak transcription	Right Ventricle	heart
11	chr7:129487200-129502400	Weak transcription	Ovary	ovary
12	chr7:129488200-129499600	Weak transcription	Left Ventricle	heart
13	chr7:129491600-129510000	Weak transcription	Fetal Intestine Large	intestine
14	chr7:129491800-129502000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:129492000-129499400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:129492000-129501200	Weak transcription	Stomach Mucosa	stomach
17	chr7:129492000-129509200	Weak transcription	Fetal Intestine Small	intestine
18	chr7:129492200-129501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:129492200-129502400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:129492600-129502400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:129493000-129500800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:129493800-129499600	Weak transcription	Spleen	Spleen
23	chr7:129493800-129502400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:129493800-129502400	Weak transcription	HSMMtube	muscle
25	chr7:129493800-129510400	Weak transcription	Brain Germinal Matrix	brain
26	chr7:129494400-129499400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:129494400-129499800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:129494400-129502200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:129494400-129502400	Weak transcription	Brain Angular Gyrus	brain
30	chr7:129494400-129502400	Weak transcription	Gastric	stomach
31	chr7:129494400-129518800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:129495000-129500600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:129495000-129502000	Weak transcription	Fetal Kidney	kidney
34	chr7:129495400-129510400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:129495600-129500600	Weak transcription	HUVEC	blood vessel
36	chr7:129495600-129502400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:129495600-129517000	Weak transcription	Fetal Lung	lung
38	chr7:129495800-129499600	Weak transcription	Fetal Brain Male	brain
39	chr7:129496200-129500000	Weak transcription	A549	lung
40	chr7:129496200-129500000	Enhancers	NHDF-Ad	bronchial
41	chr7:129496200-129505600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr7:129496200-129509400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr7:129496400-129500800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:129496400-129520400	Weak transcription	Fetal Brain Female	brain
45	chr7:129496800-129499600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:129496800-129499600	Weak transcription	Pancreas	Pancrea
47	chr7:129496800-129499600	Weak transcription	Psoas Muscle	Psoas
48	chr7:129496800-129499600	Weak transcription	Right Atrium	heart
49	chr7:129496800-129499600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:129496800-129499600	Weak transcription	NHLF	lung

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