Variant report

Variant	rs193590
Chromosome Location	chr7:116858384-116858385
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	EP300	chr7:116857553-116858385	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr7:116857492-116858427	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr7:116857490-116858442	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr7:116857479-116858462	SK-N-SH	brain:	n/a	chr7:116857799-116857815 chr7:116858256-116858273
5	POLR2A	chr7:116858372-116858475	ProgFib	skin:	n/a	n/a
6	PBX3	chr7:116857551-116858408	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr7:116857582-116858402	SK-N-SH	brain:	n/a	chr7:116857799-116857815 chr7:116858256-116858273

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:116610596-116619447..7:116849860-116864942	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ST7	TF binding region
ENSG00000213050	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10267855	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10267869	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10281328	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10808186	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs12690963	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193572	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs193573	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs193574	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs193575	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs193576	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs193577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193578	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs193579	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193580	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs193581	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs193583	1.00[CEU][hapmap]
rs193584	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs193586	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs193587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193591	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];0.98[ASN][1000 genomes]
rs193592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193594	0.88[CEU][hapmap];0.87[GIH][hapmap];0.87[EUR][1000 genomes]
rs193595	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs3757807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808193	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs3808194	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808195	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3808196	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6954357	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7783832	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7788285	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7802396	1.00[CEU][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831108	chr7:116749534-116952011	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv5916	chr7:116825221-116870570	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116798200-116866600	Weak transcription	HMEC	breast
2	chr7:116808400-116871800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:116824200-116867200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr7:116825400-116859600	Weak transcription	Brain Anterior Caudate	brain
5	chr7:116827800-116859000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:116828800-116865400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:116830800-116859400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:116830800-116859600	Weak transcription	Gastric	stomach
9	chr7:116831000-116870800	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:116831000-116870800	Weak transcription	Spleen	Spleen
11	chr7:116831200-116865200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:116831400-116858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:116831400-116859000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:116831400-116860400	Weak transcription	HepG2	liver
15	chr7:116831400-116861200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:116834400-116868800	Weak transcription	HSMM	muscle
17	chr7:116835000-116871400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:116838800-116859600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:116839000-116868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:116840000-116859000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:116840000-116871800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:116840600-116859600	Weak transcription	Lung	lung
23	chr7:116840800-116860800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:116840800-116861000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:116842800-116865200	Weak transcription	NHEK	skin
26	chr7:116844000-116872600	Weak transcription	Right Ventricle	heart
27	chr7:116847800-116867000	Weak transcription	A549	lung
28	chr7:116849000-116859600	Weak transcription	Brain Angular Gyrus	brain
29	chr7:116849400-116872000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr7:116850600-116859400	Weak transcription	Brain Substantia Nigra	brain
31	chr7:116850600-116859600	Weak transcription	Esophagus	oesophagus
32	chr7:116850600-116862200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:116850600-116863000	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:116850800-116858800	Weak transcription	Fetal Intestine Small	intestine
35	chr7:116850800-116859200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:116850800-116859400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:116850800-116859400	Weak transcription	Aorta	Aorta
38	chr7:116850800-116859400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:116850800-116860000	Weak transcription	Pancreas	Pancrea
40	chr7:116850800-116869200	Weak transcription	Psoas Muscle	Psoas
41	chr7:116851000-116859400	Weak transcription	Adipose Nuclei	Adipose
42	chr7:116851000-116859600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:116851000-116860800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:116851000-116863200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:116851200-116859200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr7:116851200-116859200	Weak transcription	Ovary	ovary
47	chr7:116851200-116859400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:116851200-116859400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:116851200-116859400	Weak transcription	HSMMtube	muscle
50	chr7:116851200-116859600	Weak transcription	Fetal Intestine Large	intestine

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