Variant report

Variant	rs12194823
Chromosome Location	chr6:38052296-38052297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38049801..38051857-chr6:38052052..38053726,3	MCF-7	breast:
2	chr6:38043781..38045291-chr6:38051092..38053628,2	MCF-7	breast:
3	chr6:38051591..38053577-chr6:38056033..38058165,2	K562	blood:
4	chr6:38046808..38049767-chr6:38051666..38053888,2	K562	blood:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10456097	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947712	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947713	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190306	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194618	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212723	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213151	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214375	0.92[EUR][1000 genomes]
rs13214465	0.82[EUR][1000 genomes]
rs13220131	0.80[EUR][1000 genomes]
rs1569657	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16890344	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132597	0.82[EUR][1000 genomes]
rs2281266	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2645102	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645113	0.86[EUR][1000 genomes]
rs2645116	0.83[EUR][1000 genomes]
rs2645120	0.80[EUR][1000 genomes]
rs2645127	0.83[EUR][1000 genomes]
rs2645128	0.84[EUR][1000 genomes]
rs2645131	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2645134	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2645137	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842500	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842527	0.83[EUR][1000 genomes]
rs2842529	0.86[EUR][1000 genomes]
rs34952988	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35257826	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140804	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747130	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941850	0.93[EUR][1000 genomes];0.96[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:112 , 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	chr6:38032400-38056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:38033000-38052600	Weak transcription	Lung	lung
14	chr6:38033000-38063400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:38035000-38084000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:38036400-38075000	Weak transcription	Thymus	Thymus
17	chr6:38037200-38052400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:38042800-38060000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:38045400-38058800	Weak transcription	Fetal Kidney	kidney
20	chr6:38045600-38055600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:38045800-38058600	Weak transcription	Fetal Lung	lung
23	chr6:38045800-38059400	Weak transcription	Fetal Heart	heart
24	chr6:38045800-38059600	Weak transcription	Aorta	Aorta
25	chr6:38045800-38079800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:38046000-38084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:38046200-38062600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:38046400-38063200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:38046600-38074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:38047000-38062800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:38047200-38058600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:38047200-38058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:38047400-38058800	Weak transcription	Brain Angular Gyrus	brain
34	chr6:38047600-38076200	Weak transcription	Fetal Stomach	stomach
35	chr6:38047800-38055000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:38047800-38057400	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:38047800-38062400	Weak transcription	HepG2	liver
38	chr6:38048000-38054000	Weak transcription	Fetal Brain Male	brain
39	chr6:38048000-38060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:38048000-38073000	Weak transcription	Small Intestine	intestine
41	chr6:38048200-38056400	Weak transcription	K562	blood
42	chr6:38048400-38056400	Strong transcription	Primary B cells from cord blood	blood
43	chr6:38048600-38054800	Weak transcription	Colonic Mucosa	Colon
44	chr6:38048800-38055200	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:38048800-38055600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:38048800-38055600	Weak transcription	Brain Substantia Nigra	brain
47	chr6:38049000-38052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:38049000-38056200	Weak transcription	Brain Anterior Caudate	brain
49	chr6:38049000-38060800	Weak transcription	A549	lung
50	chr6:38049000-38061200	Weak transcription	NHDF-Ad	bronchial

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