Variant report

Variant	rs3731673
Chromosome Location	chr2:20240668-20240669
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20239516..20241973-chr2:20242633..20244328,2	MCF-7	breast:
2	chr2:20239173..20241754-chr3:122981267..122982914,2	MCF-7	breast:
3	chr2:20233000..20234646-chr2:20240342..20243953,3	MCF-7	breast:
4	chr2:20239886..20242737-chr2:20245046..20246984,2	K562	blood:
5	chr2:20236235..20238092-chr2:20238674..20240856,2	MCF-7	breast:
6	chr2:20226527..20228627-chr2:20238902..20240937,2	K562	blood:
7	chr2:20235025..20246171-chr2:20248104..20254249,17	MCF-7	breast:
8	chr2:20239345..20241750-chr2:20293079..20295990,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068697	Chromatin interaction
ENSG00000223734	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1016316	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11674251	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.89[MKK][hapmap];0.85[ASN][1000 genomes]
rs11679737	0.86[ASW][hapmap]
rs11689320	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689431	1.00[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs11694170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11695154	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1191805	0.85[EUR][1000 genomes]
rs1191817	0.85[EUR][1000 genomes]
rs12988954	0.94[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1473887	0.82[AMR][1000 genomes]
rs1473890	0.93[EUR][1000 genomes]
rs1513830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16987338	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34539547	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35030383	0.81[ASN][1000 genomes]
rs36071721	0.92[EUR][1000 genomes]
rs3769759	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109431	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6709349	0.86[ASW][hapmap]
rs6720508	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558777	0.91[EUR][1000 genomes]
rs7558988	0.89[EUR][1000 genomes]
rs7570360	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587612	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs878983	0.86[ASW][hapmap];0.89[MKK][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3731673	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20221400-20249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:20227000-20240800	Strong transcription	Placenta	Placenta
3	chr2:20227000-20241000	Strong transcription	Liver	Liver
4	chr2:20227000-20242000	Strong transcription	Primary T cells from cord blood	blood
5	chr2:20227000-20242400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:20227200-20240800	Strong transcription	Fetal Lung	lung
7	chr2:20227200-20241000	Strong transcription	Fetal Thymus	thymus
8	chr2:20227200-20242200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:20227400-20240800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:20227400-20240800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:20227400-20240800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:20227600-20241000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:20227800-20241200	Strong transcription	Fetal Intestine Large	intestine
14	chr2:20227800-20242200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:20228000-20242000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:20228200-20240800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr2:20228200-20240800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:20228200-20242600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:20228400-20240800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:20228400-20241400	Strong transcription	Dnd41	blood
21	chr2:20228800-20240800	Strong transcription	Brain Anterior Caudate	brain
22	chr2:20229600-20240800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:20229800-20240800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:20229800-20241400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:20230000-20242200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:20230200-20241600	Strong transcription	HepG2	liver
27	chr2:20230200-20241800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr2:20230200-20242200	Strong transcription	Fetal Brain Female	brain
29	chr2:20230400-20240800	Strong transcription	Brain Germinal Matrix	brain
30	chr2:20230400-20241400	Strong transcription	A549	lung
31	chr2:20230400-20241600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:20230400-20242200	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:20230600-20242600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:20230600-20248000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:20230800-20240800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:20230800-20241200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:20232800-20241600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:20233200-20240800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:20233200-20240800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr2:20233200-20240800	Strong transcription	Fetal Stomach	stomach
41	chr2:20233200-20241400	Strong transcription	Thymus	Thymus
42	chr2:20234800-20248200	Weak transcription	Psoas Muscle	Psoas
43	chr2:20235000-20240800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:20235000-20248000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:20235400-20240800	Strong transcription	Fetal Kidney	kidney
46	chr2:20235400-20247400	Weak transcription	Fetal Brain Male	brain
47	chr2:20235800-20241600	Strong transcription	Brain Angular Gyrus	brain
48	chr2:20236400-20241200	Weak transcription	Stomach Mucosa	stomach
49	chr2:20236400-20242800	Weak transcription	Right Atrium	heart
50	chr2:20236600-20241400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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