Variant report

Variant	rs17649606
Chromosome Location	chr6:38050376-38050377
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	chr6:38049801..38051857-chr6:38052052..38053726,3	MCF-7	breast:
2	chr6:38048909..38051360-chr6:38060879..38063645,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11751393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11753390	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11753809	0.85[ASN][1000 genomes]
rs11755262	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11755824	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757371	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11757622	0.85[ASN][1000 genomes]
rs11759754	0.85[ASN][1000 genomes]
rs13552	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16890376	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890395	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17648097	0.85[ASN][1000 genomes]
rs17648634	0.85[ASN][1000 genomes]
rs17648699	0.85[ASN][1000 genomes]
rs17649630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55898002	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56100831	0.85[ASN][1000 genomes]
rs56136126	0.85[ASN][1000 genomes]
rs59522592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59810748	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61521259	0.85[ASN][1000 genomes]
rs61705055	0.85[ASN][1000 genomes]
rs68148876	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6925259	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6930340	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72850806	0.85[ASN][1000 genomes]
rs72850831	0.85[ASN][1000 genomes]
rs72850855	0.85[ASN][1000 genomes]
rs72850856	0.85[ASN][1000 genomes]
rs72850871	0.85[ASN][1000 genomes]
rs72852516	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs72852536	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72852555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72852565	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852588	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994530	1.00[AFR][1000 genomes];0.85[ASN][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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38017200-38055000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38023000-38054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:38023200-38052800	Weak transcription	Gastric	stomach
4	chr6:38026200-38053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:38031400-38052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:38031600-38053200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:38031600-38059600	Weak transcription	Spleen	Spleen
9	chr6:38031600-38061600	Weak transcription	Brain Germinal Matrix	brain
10	chr6:38032000-38052600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:38032000-38052600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:38032200-38051400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:38032400-38050800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:38032400-38056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:38033000-38051200	Weak transcription	Fetal Intestine Large	intestine
16	chr6:38033000-38052600	Weak transcription	Lung	lung
17	chr6:38033000-38063400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:38033200-38051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:38033600-38050800	Weak transcription	Placenta	Placenta
20	chr6:38034200-38051200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:38035000-38084000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:38035200-38051000	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:38035400-38050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:38035800-38050400	Weak transcription	GM12878-XiMat	blood
25	chr6:38035800-38051000	Weak transcription	Ovary	ovary
26	chr6:38036400-38075000	Weak transcription	Thymus	Thymus
27	chr6:38037200-38052400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:38042800-38060000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:38043200-38050800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:38043200-38051000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:38045400-38051400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:38045400-38058800	Weak transcription	Fetal Kidney	kidney
33	chr6:38045600-38055600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:38045800-38051000	Weak transcription	Pancreas	Pancrea
36	chr6:38045800-38058600	Weak transcription	Fetal Lung	lung
37	chr6:38045800-38059400	Weak transcription	Fetal Heart	heart
38	chr6:38045800-38059600	Weak transcription	Aorta	Aorta
39	chr6:38045800-38079800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:38046000-38084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:38046200-38062600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:38046400-38063200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:38046600-38074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:38047000-38062800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:38047200-38058600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:38047200-38058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:38047400-38058800	Weak transcription	Brain Angular Gyrus	brain
48	chr6:38047600-38051000	Weak transcription	Esophagus	oesophagus
49	chr6:38047600-38051400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:38047600-38076200	Weak transcription	Fetal Stomach	stomach

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