Variant report

Variant	rs12005177
Chromosome Location	chr9:103076208-103076209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103062847..103065404-chr9:103075501..103077702,2	MCF-7	breast:
2	chr9:103075126..103077245-chr9:103111933..103114024,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10819755	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10819757	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10819758	1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819760	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819765	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819766	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819768	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989041	0.96[EUR][1000 genomes]
rs10989046	0.96[EUR][1000 genomes]
rs10989047	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989050	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989051	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989062	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989063	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989068	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989069	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989072	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989074	1.00[CHB][hapmap]
rs10989077	1.00[ASN][1000 genomes]
rs11515449	0.94[EUR][1000 genomes]
rs11515542	0.94[EUR][1000 genomes]
rs11788648	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790431	0.96[EUR][1000 genomes]
rs11791637	0.81[EUR][1000 genomes]
rs11791943	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793726	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794753	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11795004	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003468	0.96[EUR][1000 genomes]
rs12352336	1.00[ASN][1000 genomes]
rs12375859	1.00[ASN][1000 genomes]
rs12379480	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919024	0.96[EUR][1000 genomes]
rs17813447	1.00[YRI][hapmap]
rs3199998	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274951	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274961	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579387	1.00[ASN][1000 genomes]
rs7028101	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036972	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037122	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037419	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039994	0.96[EUR][1000 genomes]
rs7849019	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866700	0.94[EUR][1000 genomes]
rs7873560	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874036	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
2	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
4	chr9:103048000-103078000	Strong transcription	Primary T cells from cord blood	blood
5	chr9:103048400-103083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:103050600-103086400	Strong transcription	Dnd41	blood
7	chr9:103050800-103080400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:103051000-103088800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:103051200-103078000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:103055800-103077600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
12	chr9:103058400-103092200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:103058800-103084800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:103063800-103093400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:103063800-103106000	Weak transcription	Esophagus	oesophagus
16	chr9:103064000-103100000	Weak transcription	Colonic Mucosa	Colon
17	chr9:103064200-103093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:103064600-103079400	Weak transcription	HSMMtube	muscle
19	chr9:103064800-103104200	Weak transcription	Right Ventricle	heart
20	chr9:103065000-103080600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:103065200-103087600	Weak transcription	Brain Anterior Caudate	brain
23	chr9:103065400-103080200	Weak transcription	Brain Substantia Nigra	brain
24	chr9:103065400-103087400	Weak transcription	Psoas Muscle	Psoas
25	chr9:103066200-103080200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:103066200-103087800	Weak transcription	Gastric	stomach
27	chr9:103066200-103088400	Weak transcription	Lung	lung
28	chr9:103066200-103100400	Weak transcription	Aorta	Aorta
29	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
30	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
31	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:103066400-103079400	Weak transcription	HUVEC	blood vessel
33	chr9:103066600-103080400	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:103066800-103091600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:103067000-103086600	Strong transcription	Primary B cells from cord blood	blood
36	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
37	chr9:103067800-103080800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:103068000-103077400	Weak transcription	Liver	Liver
39	chr9:103068200-103080400	Weak transcription	Brain Angular Gyrus	brain
40	chr9:103068200-103085200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:103068200-103094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:103068600-103077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:103069200-103095400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:103069400-103094800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:103069800-103078400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:103069800-103078800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:103069800-103092000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:103070000-103093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:103070400-103078800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr9:103070600-103086800	Strong transcription	HepG2	liver

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