Variant report

Variant	rs9904021
Chromosome Location	chr17:38399230-38399231
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	NFIC	chr17:38399002-38399541	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr17:38398938-38399585	SK-N-SH	brain:	n/a	n/a
3	EP300	chr17:38398990-38399462	SK-N-SH_RA	brain:	n/a	n/a
4	PBX3	chr17:38398968-38399539	SK-N-SH	brain:	n/a	n/a
5	EP300	chr17:38398973-38399248	SK-N-SH_RA	brain:	n/a	n/a
6	TCF12	chr17:38399002-38399624	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr17:38398919-38399504	SK-N-SH	brain:	n/a	n/a
8	EP300	chr17:38398695-38399881	SK-N-SH	brain:	n/a	chr17:38399700-38399714
9	MXI1	chr17:38398714-38399803	SK-N-SH	brain:	n/a	n/a
10	JUND	chr17:38398859-38399647	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr17:38399019-38399358	SH-SY5Y	brain:	n/a	n/a
12	GATA3	chr17:38398973-38399481	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38359009..38361082-chr17:38396610..38399258,3	MCF-7	breast:

Variant related genes	Relation type
RNY4P8	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11078939	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078940	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12944717	0.84[ASN][1000 genomes]
rs12946680	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs13706	0.81[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs16965666	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs16965687	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2077464	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2120200	0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs2280400	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap]
rs2314338	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs28537537	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28663197	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35286757	0.84[EUR][1000 genomes]
rs36030243	0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs3744806	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4077125	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4134994	0.92[EUR][1000 genomes]
rs4566234	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55767073	0.80[AMR][1000 genomes]
rs55835834	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56013073	0.82[AMR][1000 genomes]
rs56029626	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57179137	0.91[EUR][1000 genomes]
rs58822685	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs59018914	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59490243	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59861136	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60220138	0.91[ASN][1000 genomes]
rs61024420	0.82[ASN][1000 genomes]
rs6503539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67597966	0.84[ASN][1000 genomes]
rs7211770	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7217852	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs72836634	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72836635	0.84[ASN][1000 genomes]
rs72836636	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72836639	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72836640	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72836641	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72836642	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72836648	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72836651	0.91[ASN][1000 genomes]
rs72836653	0.91[ASN][1000 genomes]
rs72836656	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72836660	0.91[ASN][1000 genomes]
rs7359537	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73983025	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7405635	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs8066144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs8073925	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs8078204	0.87[ASN][1000 genomes]
rs8078226	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8080931	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8082192	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs9303285	1.00[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs9303286	0.85[CEU][hapmap]
rs9891694	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9891718	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9892404	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9892946	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9893520	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895163	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897092	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901109	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9904270	0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs9906409	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9907683	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs9908034	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9908257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9910197	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9910788	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9911840	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9912082	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9914531	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9916460	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9916782	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[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	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv522863	chr17:38388040-38405037	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv525961	chr17:38388040-38405037	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38376600-38400400	Weak transcription	Psoas Muscle	Psoas
2	chr17:38376600-38412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:38376600-38416800	Weak transcription	Aorta	Aorta
4	chr17:38377000-38418400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:38377200-38404800	Weak transcription	HSMMtube	muscle
6	chr17:38377400-38408000	Weak transcription	Small Intestine	intestine
7	chr17:38377600-38412800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:38377800-38400400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr17:38379200-38413000	Weak transcription	Pancreas	Pancrea
10	chr17:38381200-38412400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:38381400-38407000	Weak transcription	Hela-S3	cervix
12	chr17:38381400-38407400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr17:38381400-38407400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:38381400-38407400	Weak transcription	Osteobl	bone
15	chr17:38381800-38407600	Weak transcription	K562	blood
16	chr17:38381800-38408000	Weak transcription	Right Ventricle	heart
17	chr17:38382000-38407600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:38382000-38412400	Weak transcription	Fetal Lung	lung
19	chr17:38382800-38399400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:38385400-38407600	Weak transcription	NHEK	skin
21	chr17:38386000-38407800	Weak transcription	Adipose Nuclei	Adipose
22	chr17:38387600-38400200	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:38389800-38407600	Weak transcription	NH-A	brain
24	chr17:38390200-38412200	Weak transcription	HepG2	liver
25	chr17:38390200-38413000	Weak transcription	Colonic Mucosa	Colon
26	chr17:38390400-38407400	Weak transcription	HUVEC	blood vessel
27	chr17:38390800-38416600	Weak transcription	Gastric	stomach
28	chr17:38391000-38401200	Weak transcription	Liver	Liver
29	chr17:38391000-38407000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr17:38391000-38407600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:38391000-38408000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:38391000-38409800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:38391000-38412400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr17:38391000-38412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:38391000-38412600	Weak transcription	Placenta	Placenta
36	chr17:38391200-38400000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:38391200-38400200	Weak transcription	GM12878-XiMat	blood
38	chr17:38391200-38400400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr17:38391200-38403000	Weak transcription	Thymus	Thymus
40	chr17:38391200-38404600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:38391200-38407600	Weak transcription	A549	lung
42	chr17:38391200-38408000	Weak transcription	Ovary	ovary
43	chr17:38391200-38412200	Weak transcription	Fetal Thymus	thymus
44	chr17:38391200-38412600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:38391200-38412600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:38391200-38413600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr17:38391200-38416800	Weak transcription	Esophagus	oesophagus
48	chr17:38391400-38413600	Weak transcription	Spleen	Spleen
49	chr17:38391400-38414600	Weak transcription	Primary B cells from cord blood	blood
50	chr17:38391600-38404800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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