Variant report

Variant	rs638407
Chromosome Location	chr6:149738350-149738351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149733372..149735281-chr6:149738078..149740684,2	K562	blood:
2	chr6:149727796..149730556-chr6:149737102..149739514,2	K562	blood:
3	chr6:149639557..149641696-chr6:149736271..149738356,2	MCF-7	breast:
4	chr6:149401024..149403693-chr6:149738152..149741655,3	K562	blood:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs11155640	0.81[YRI][hapmap]
rs11155642	0.81[YRI][hapmap]
rs11155645	0.83[YRI][hapmap]
rs11155647	0.83[YRI][hapmap]
rs12191079	0.81[YRI][hapmap]
rs12204461	0.83[YRI][hapmap]
rs12204793	0.83[YRI][hapmap]
rs12211357	0.82[YRI][hapmap]
rs17506789	0.86[YRI][hapmap]
rs1980774	0.81[YRI][hapmap]
rs2143076	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179367	0.92[EUR][1000 genomes]
rs2262617	0.95[EUR][1000 genomes]
rs2341783	0.87[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744432	0.84[AMR][1000 genomes]
rs2744434	0.87[JPT][hapmap]
rs2789488	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789490	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs2789492	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs3734296	0.87[JPT][hapmap]
rs472810	0.86[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs478767	0.87[JPT][hapmap]
rs480526	0.87[JPT][hapmap]
rs489551	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4895788	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4895789	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs4897124	0.95[EUR][1000 genomes]
rs4897125	0.93[EUR][1000 genomes]
rs492956	0.86[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.83[JPT][hapmap]
rs504985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs506268	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs511100	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs511105	0.87[JPT][hapmap]
rs514839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs515133	0.83[JPT][hapmap]
rs521845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs527971	0.80[JPT][hapmap]
rs532250	0.83[JPT][hapmap]
rs536203	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs537354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs538386	0.87[JPT][hapmap]
rs540538	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs544947	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs556335	0.87[JPT][hapmap]
rs559052	0.86[JPT][hapmap]
rs560051	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs562428	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs564961	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs565825	0.86[JPT][hapmap]
rs570442	0.83[JPT][hapmap]
rs577001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs579789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs580011	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs585022	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs600739	0.81[JPT][hapmap]
rs628488	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652921	0.87[JPT][hapmap]
rs6570965	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs663625	0.87[JPT][hapmap]
rs6911411	0.81[YRI][hapmap]
rs6920383	0.80[YRI][hapmap]
rs6932778	0.81[YRI][hapmap]
rs7349921	0.86[YRI][hapmap]
rs763590	0.82[YRI][hapmap]
rs7896	0.83[YRI][hapmap]
rs909793	0.81[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9285519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9285520	0.81[YRI][hapmap]
rs9322178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9373589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373592	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377212	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377218	0.87[CHB][hapmap];0.96[JPT][hapmap];0.92[ASN][1000 genomes]
rs9390676	0.86[JPT][hapmap]
rs9390677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9404034	0.87[JPT][hapmap]
rs9498322	0.83[YRI][hapmap]
rs9498323	0.85[YRI][hapmap]
rs9498324	0.81[YRI][hapmap]
rs9498325	0.83[YRI][hapmap]
rs9498332	0.83[YRI][hapmap]
rs9498333	0.83[YRI][hapmap]
rs9498335	0.81[YRI][hapmap]
rs9498336	0.83[YRI][hapmap]
rs9498337	0.83[YRI][hapmap]
rs9498338	0.82[YRI][hapmap]
rs9498341	0.82[YRI][hapmap]
rs9498342	0.81[YRI][hapmap]
rs997682	0.81[YRI][hapmap]

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	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149709600-149750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:149721800-149743800	Weak transcription	Lung	lung
3	chr6:149721800-149744800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:149721800-149745200	Weak transcription	Pancreas	Pancrea
5	chr6:149722000-149745000	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:149725200-149744600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:149728200-149744600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:149730600-149744400	Weak transcription	NHDF-Ad	bronchial
9	chr6:149731400-149738800	Weak transcription	A549	lung
10	chr6:149731400-149743800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:149731600-149738800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:149731600-149744200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:149731600-149744400	Weak transcription	Brain Anterior Caudate	brain
14	chr6:149731600-149744600	Weak transcription	NHLF	lung
15	chr6:149731600-149745200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:149731600-149745200	Weak transcription	Left Ventricle	heart
17	chr6:149731600-149745200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:149731800-149744400	Weak transcription	Brain Substantia Nigra	brain
19	chr6:149731800-149744400	Weak transcription	HSMMtube	muscle
20	chr6:149731800-149745200	Weak transcription	Fetal Brain Female	brain
21	chr6:149732000-149738400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:149732000-149744400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:149732000-149744600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:149732200-149738400	Weak transcription	Brain Angular Gyrus	brain
25	chr6:149732200-149744400	Weak transcription	Ovary	ovary
26	chr6:149732200-149744400	Weak transcription	Osteobl	bone
27	chr6:149732200-149745000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:149732400-149740800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:149732400-149744000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:149732400-149744400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:149732400-149744400	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:149732400-149745200	Weak transcription	Brain Germinal Matrix	brain
33	chr6:149732600-149743800	Weak transcription	Placenta	Placenta
34	chr6:149732600-149744600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:149732600-149744600	Weak transcription	Fetal Lung	lung
36	chr6:149732600-149744800	Weak transcription	NH-A	brain
37	chr6:149732600-149745400	Weak transcription	Dnd41	blood
38	chr6:149732800-149744600	Weak transcription	HSMM	muscle
39	chr6:149732800-149744800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:149733200-149744800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:149733400-149740800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:149733400-149744600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:149733400-149744800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:149733600-149738600	Weak transcription	Primary T cells from cord blood	blood
45	chr6:149733600-149744800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:149733800-149740000	Weak transcription	GM12878-XiMat	blood
47	chr6:149735000-149744400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:149735200-149740800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:149735400-149744400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:149735600-149739000	Weak transcription	Primary hematopoietic stem cells	blood

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