Variant report

Variant	rs2038477
Chromosome Location	chr6:71573109-71573110
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	chr6:71548845..71551416-chr6:71572319..71574307,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13197338	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs13212771	0.88[JPT][hapmap]
rs2460692	0.81[GIH][hapmap];0.89[JPT][hapmap]
rs2460699	0.82[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2474914	0.81[GIH][hapmap];0.89[JPT][hapmap]
rs2474915	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2474916	0.92[CEU][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes]
rs2474921	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap]
rs2504748	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2504749	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2504750	0.94[JPT][hapmap]
rs2504751	0.89[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs2504752	0.94[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2504753	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734371	0.89[JPT][hapmap]
rs3734372	0.89[JPT][hapmap]
rs483894	0.89[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.82[EUR][1000 genomes]
rs576516	0.85[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];0.83[EUR][1000 genomes]
rs746121	0.93[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];0.84[EUR][1000 genomes]
rs9680	0.83[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038477	FAM135A	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71537600-71574200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:71550000-71575400	Weak transcription	Ovary	ovary
3	chr6:71552400-71574200	Weak transcription	HSMM	muscle
4	chr6:71554400-71574400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:71556600-71574400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:71558800-71575000	Weak transcription	HUVEC	blood vessel
7	chr6:71559000-71573800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:71559400-71573800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:71560600-71574200	Weak transcription	Brain Germinal Matrix	brain
10	chr6:71561200-71573400	Weak transcription	HMEC	breast
11	chr6:71561600-71574000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:71563400-71573600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:71564000-71575800	Weak transcription	Right Ventricle	heart
14	chr6:71566400-71574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:71568000-71574000	Weak transcription	Fetal Stomach	stomach
16	chr6:71568400-71574200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:71569000-71575600	Weak transcription	Gastric	stomach
18	chr6:71569200-71574200	Weak transcription	Fetal Thymus	thymus
19	chr6:71569200-71574400	Weak transcription	HSMMtube	muscle
20	chr6:71569200-71574600	Weak transcription	Esophagus	oesophagus
21	chr6:71569200-71574600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:71569400-71573200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:71569400-71573200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:71570000-71573800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:71570200-71573400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:71570200-71574000	Weak transcription	Left Ventricle	heart
27	chr6:71570200-71574200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:71570200-71574200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:71570600-71573200	Weak transcription	Fetal Intestine Large	intestine
30	chr6:71570800-71573200	Weak transcription	Placenta	Placenta
31	chr6:71570800-71574200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:71571400-71573200	Weak transcription	Dnd41	blood
33	chr6:71571400-71573400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:71571400-71573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:71571400-71573400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:71571400-71574000	Weak transcription	Primary T cells from cord blood	blood
37	chr6:71571400-71574200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:71571400-71575000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:71571600-71573200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:71571600-71573400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr6:71571600-71573400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:71571600-71573600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:71571600-71573600	Weak transcription	Aorta	Aorta
44	chr6:71571600-71573800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:71571600-71574000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:71571600-71574600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:71571600-71574600	Weak transcription	Primary B cells from cord blood	blood
48	chr6:71571600-71574600	Weak transcription	Adipose Nuclei	Adipose
49	chr6:71571600-71576400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:71571600-71584000	Weak transcription	Pancreas	Pancrea

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