Variant report

Variant	rs34051646
Chromosome Location	chr2:173456679-173456680
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173456525..173460577-chr2:173461176..173464180,4	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1010752	0.81[ASN][1000 genomes]
rs10181851	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1075638	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10930561	0.81[ASN][1000 genomes]
rs10930562	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930563	0.83[ASN][1000 genomes]
rs10930565	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097478	0.83[ASN][1000 genomes]
rs1133602	0.92[ASN][1000 genomes]
rs11891127	0.83[AFR][1000 genomes]
rs11904158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476204	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12693008	0.89[ASN][1000 genomes]
rs13015260	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13019331	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024563	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13385403	0.83[AFR][1000 genomes]
rs13401676	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1530864	0.87[ASN][1000 genomes]
rs1530865	0.87[ASN][1000 genomes]
rs1531150	0.85[ASN][1000 genomes]
rs16860693	0.87[ASN][1000 genomes]
rs16860697	0.83[AFR][1000 genomes]
rs16860737	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16860741	0.93[ASN][1000 genomes]
rs1868901	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1869923	0.90[ASN][1000 genomes]
rs2290564	0.83[AFR][1000 genomes]
rs2599260	0.90[ASN][1000 genomes]
rs2599261	0.90[ASN][1000 genomes]
rs2599262	0.90[ASN][1000 genomes]
rs2599263	0.90[ASN][1000 genomes]
rs2599264	0.90[ASN][1000 genomes]
rs2599265	0.90[ASN][1000 genomes]
rs2599266	0.90[ASN][1000 genomes]
rs2606062	0.90[ASN][1000 genomes]
rs2606063	0.90[ASN][1000 genomes]
rs2606064	0.89[ASN][1000 genomes]
rs2606065	0.90[ASN][1000 genomes]
rs2606066	0.90[ASN][1000 genomes]
rs2606067	0.90[ASN][1000 genomes]
rs2606070	0.90[ASN][1000 genomes]
rs35892983	0.91[ASN][1000 genomes]
rs3765065	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769321	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61505737	0.87[ASN][1000 genomes]
rs62167835	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66460331	0.82[AFR][1000 genomes]
rs6710129	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723872	0.83[AFR][1000 genomes]
rs6731354	0.82[ASN][1000 genomes]
rs6733679	0.90[ASN][1000 genomes]
rs6738196	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752386	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs70937083	0.87[ASN][1000 genomes]
rs70937084	0.87[ASN][1000 genomes]
rs7584769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179584	0.81[ASN][1000 genomes]
rs836590	0.90[ASN][1000 genomes]
rs836608	0.84[ASN][1000 genomes]
rs836614	0.84[ASN][1000 genomes]
rs836616	0.84[ASN][1000 genomes]
rs836617	0.84[ASN][1000 genomes]
rs836629	0.90[ASN][1000 genomes]
rs836630	0.90[ASN][1000 genomes]
rs836631	0.90[ASN][1000 genomes]
rs836634	0.90[ASN][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	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv3035	chr2:173419058-173463901	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv875415	chr2:173444462-173501069	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv875416	chr2:173444462-173504674	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173421800-173465200	Weak transcription	Small Intestine	intestine
2	chr2:173426200-173460600	Weak transcription	HSMMtube	muscle
3	chr2:173430600-173461600	Weak transcription	Right Ventricle	heart
4	chr2:173431400-173480600	Weak transcription	Gastric	stomach
5	chr2:173432000-173462400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:173439800-173458000	Weak transcription	NHDF-Ad	bronchial
7	chr2:173440200-173458200	Weak transcription	Osteobl	bone
8	chr2:173440200-173467600	Weak transcription	NH-A	brain
9	chr2:173443200-173472200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:173443800-173463200	Weak transcription	A549	lung
11	chr2:173444000-173464000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:173444200-173470400	Weak transcription	Psoas Muscle	Psoas
13	chr2:173444400-173480200	Strong transcription	HepG2	liver
14	chr2:173444600-173465400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:173445200-173463200	Weak transcription	Fetal Brain Female	brain
16	chr2:173445400-173461000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:173445400-173462600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:173445400-173471000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:173446400-173460400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:173447800-173460200	Weak transcription	HUVEC	blood vessel
21	chr2:173448000-173463400	Weak transcription	Stomach Mucosa	stomach
22	chr2:173448200-173459000	Weak transcription	Brain Germinal Matrix	brain
23	chr2:173449400-173460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:173449400-173462400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:173449800-173462800	Strong transcription	Primary B cells from cord blood	blood
26	chr2:173451200-173465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:173451600-173462800	Strong transcription	Primary T cells from cord blood	blood
28	chr2:173451600-173463400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:173451800-173460200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:173451800-173471800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:173452000-173460000	Weak transcription	Ovary	ovary
32	chr2:173452000-173479800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:173452200-173462400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:173452200-173463600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:173452400-173469400	Weak transcription	Lung	lung
36	chr2:173452800-173462800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:173452800-173462800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:173452800-173478000	Weak transcription	Fetal Brain Male	brain
39	chr2:173452800-173478600	Weak transcription	Spleen	Spleen
40	chr2:173453600-173457800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:173453800-173457600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:173453800-173458200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:173453800-173459400	Weak transcription	Hela-S3	cervix
44	chr2:173453800-173459600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:173453800-173461200	Weak transcription	Fetal Heart	heart
46	chr2:173453800-173463400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:173453800-173472400	Weak transcription	Brain Angular Gyrus	brain
48	chr2:173453800-173478600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:173454000-173463800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:173454000-173464200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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