Variant report

Variant	rs10207640
Chromosome Location	chr2:173307726-173307727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173290118..173293854-chr2:173304445..173308429,5	MCF-7	breast:
2	chr2:173305651..173308111-chr2:173326516..173329013,2	MCF-7	breast:
3	chr2:173297263..173301573-chr2:173305902..173308346,3	MCF-7	breast:
4	chr2:173305610..173308515-chr2:173310023..173312671,2	MCF-7	breast:
5	chr2:173307073..173308885-chr2:173311042..173312605,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091409	Chromatin interaction
ENSG00000226963	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10187564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195932	1.00[ASW][hapmap]
rs10197251	0.85[YRI][hapmap]
rs10207654	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];1.00[MKK][hapmap];1.00[TSI][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]
rs10210544	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10930559	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12052385	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12053442	0.85[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12615584	0.85[EUR][1000 genomes]
rs12615596	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12621278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622724	1.00[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13410475	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]
rs13414928	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13421350	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs1574256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1574259	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16860397	1.00[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16860416	1.00[JPT][hapmap]
rs16860419	1.00[EUR][1000 genomes]
rs16860426	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860438	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860634	1.00[CEU][hapmap]
rs2293645	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs2293648	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs28485589	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762618	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]
rs4405725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55867175	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56882727	0.85[EUR][1000 genomes]
rs56892098	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57244773	0.85[EUR][1000 genomes]
rs57404607	0.85[EUR][1000 genomes]
rs57587465	0.85[EUR][1000 genomes]
rs57878744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59374567	0.85[EUR][1000 genomes]
rs59454075	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59970483	0.85[EUR][1000 genomes]
rs60096331	0.85[EUR][1000 genomes]
rs6726739	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs6730284	0.85[EUR][1000 genomes]
rs6741759	0.85[EUR][1000 genomes]
rs7564416	0.93[JPT][hapmap]
rs7607084	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9636257	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
2	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
3	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr2:173300400-173308000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr2:173301000-173308400	Enhancers	Fetal Intestine Small	intestine
6	chr2:173301200-173308400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:173301400-173308400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:173302400-173308200	Enhancers	HepG2	liver
9	chr2:173302600-173308000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr2:173303200-173308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:173303200-173309600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:173304200-173311400	Weak transcription	Liver	Liver
13	chr2:173304600-173308400	Enhancers	HSMM	muscle
14	chr2:173304600-173308800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:173304600-173310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:173304800-173308000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:173304800-173308800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:173305000-173310400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:173305400-173308000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr2:173305400-173308200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:173305400-173309000	Enhancers	Fetal Muscle Leg	muscle
23	chr2:173305800-173308800	Enhancers	Fetal Heart	heart
24	chr2:173306000-173308400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:173306200-173308200	Enhancers	Thymus	Thymus
26	chr2:173306200-173310400	Weak transcription	Fetal Lung	lung
27	chr2:173306200-173311200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:173306400-173307800	Flanking Active TSS	Hela-S3	cervix
29	chr2:173306600-173307800	Enhancers	Psoas Muscle	Psoas
30	chr2:173306600-173308200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:173306800-173307800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:173306800-173308000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr2:173306800-173309800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:173306800-173311400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:173307000-173308400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr2:173307000-173308600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr2:173307000-173308600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:173307000-173308600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr2:173307000-173309600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:173307000-173309600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:173307000-173310600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:173307200-173307800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:173307200-173307800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr2:173307200-173307800	Enhancers	NH-A	brain
46	chr2:173307200-173308000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:173307200-173308400	Enhancers	HSMMtube	muscle
48	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:173307400-173308200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:173307400-173308200	Enhancers	HMEC	breast

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