Variant report

Variant	rs17034335
Chromosome Location	chr1:9846267-9846268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9844090..9846323-chr1:9883653..9885317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10779731	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10864435	0.94[CHD][hapmap];0.81[MEX][hapmap]
rs10864436	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];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864437	0.80[EUR][1000 genomes]
rs10864438	0.82[EUR][1000 genomes]
rs11121484	0.94[CHD][hapmap];0.81[JPT][hapmap]
rs11121485	0.88[ASN][1000 genomes]
rs11121486	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs11121488	0.91[ASN][1000 genomes]
rs11121492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121493	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11674	0.82[EUR][1000 genomes]
rs11806520	0.85[EUR][1000 genomes]
rs12025864	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12034239	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034313	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12037599	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12042293	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs12047054	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap]
rs12078414	1.00[CEU][hapmap]
rs12088273	0.80[EUR][1000 genomes]
rs1220419	0.83[AMR][1000 genomes]
rs1228434	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12568720	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs12569008	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs1615629	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1660741	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1660742	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17034340	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767277	1.00[CEU][hapmap]
rs2788605	0.86[EUR][1000 genomes]
rs4512653	0.88[CHB][hapmap]
rs4585981	0.86[EUR][1000 genomes]
rs56109009	0.82[EUR][1000 genomes]
rs57480158	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6699320	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs72855716	0.82[EUR][1000 genomes]
rs72855733	0.84[EUR][1000 genomes]
rs72855735	0.86[EUR][1000 genomes]
rs7526958	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap]
rs7550246	0.82[EUR][1000 genomes]
rs7550295	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs767762	1.00[CEU][hapmap]
rs946277	0.94[EUR][1000 genomes]
rs946278	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs946279	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv2298	chr1:9826286-9857487	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1848817	chr1:9842576-9855529	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1821566	chr1:9842576-9856687	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 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	chr1:9801400-9854200	Weak transcription	Fetal Kidney	kidney
2	chr1:9811800-9857000	Weak transcription	Aorta	Aorta
3	chr1:9813800-9852200	Weak transcription	Right Atrium	heart
4	chr1:9824200-9846800	Weak transcription	Spleen	Spleen
5	chr1:9827400-9852200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:9833000-9848200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:9833400-9846400	Weak transcription	Thymus	Thymus
8	chr1:9833400-9846600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:9833400-9846800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:9833400-9846800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:9833400-9846800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:9833400-9846800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:9833400-9846800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:9833400-9846800	Weak transcription	Esophagus	oesophagus
15	chr1:9833400-9846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:9833400-9847000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:9833400-9848000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:9833400-9849200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:9833400-9851400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:9833400-9852200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:9833400-9852200	Weak transcription	Brain Angular Gyrus	brain
22	chr1:9833400-9852200	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:9833400-9852200	Weak transcription	Fetal Lung	lung
24	chr1:9833400-9852200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:9833400-9852400	Weak transcription	HSMMtube	muscle
26	chr1:9833400-9852600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:9833400-9854000	Weak transcription	Fetal Intestine Large	intestine
28	chr1:9833600-9846800	Weak transcription	Left Ventricle	heart
29	chr1:9833600-9847000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:9833600-9851400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:9833600-9851600	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:9833600-9852200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:9833600-9852200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:9833600-9852400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:9833600-9853400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:9833800-9846400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:9833800-9847000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:9833800-9848800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:9833800-9849200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:9833800-9853400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:9834000-9846800	Weak transcription	Dnd41	blood
42	chr1:9834000-9852400	Weak transcription	Brain Germinal Matrix	brain
43	chr1:9836000-9849000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:9836800-9849000	Weak transcription	Fetal Stomach	stomach
45	chr1:9836800-9852000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:9836800-9852200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:9836800-9852400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:9838000-9854400	Weak transcription	Lung	lung
49	chr1:9839400-9846800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:9839800-9853400	Weak transcription	Fetal Intestine Small	intestine

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