Variant report

Variant	rs12035998
Chromosome Location	chr1:227374760-227374761
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	chr1:227365251..227367190-chr1:227371984..227375259,3	K562	blood:
2	chr1:227373675..227376391-chr1:227377073..227380557,3	K562	blood:

Variant related genes	Relation type
ENSG00000228625	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10458379	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799411	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916098	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916117	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12033050	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12035190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12038272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12073573	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12079122	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12079173	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12080452	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095674	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097121	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1929859	0.82[ASN][1000 genomes]
rs2458523	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2482453	0.82[ASN][1000 genomes]
rs2997438	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4065211	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4551562	0.83[AMR][1000 genomes]
rs4653788	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653790	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs477373	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs482032	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs533134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs567467	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58442036	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs595155	0.80[AMR][1000 genomes]
rs61700597	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834563	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61836477	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs645081	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6660043	0.83[EUR][1000 genomes]
rs6664803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6699534	0.86[EUR][1000 genomes]
rs688718	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72757311	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7513122	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7536444	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs871210	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
4	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:227343200-227400400	Weak transcription	A549	lung
7	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
11	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:227348200-227376400	Weak transcription	Fetal Lung	lung
15	chr1:227348200-227377800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:227348200-227377800	Weak transcription	HUVEC	blood vessel
17	chr1:227348200-227379800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:227348400-227378000	Weak transcription	Liver	Liver
24	chr1:227355000-227374800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:227355400-227379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:227359200-227379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:227359400-227379800	Weak transcription	Brain Angular Gyrus	brain
29	chr1:227359400-227379800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:227359400-227379800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
32	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
33	chr1:227362800-227377600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:227362800-227377800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:227362800-227379800	Weak transcription	NHLF	lung
36	chr1:227363000-227379600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:227363800-227380600	Weak transcription	Esophagus	oesophagus
38	chr1:227364000-227379800	Weak transcription	HSMMtube	muscle
39	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
40	chr1:227364200-227381000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
42	chr1:227367200-227375400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:227369000-227379600	Weak transcription	HMEC	breast
44	chr1:227369200-227382600	Weak transcription	Fetal Brain Female	brain
45	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:227370600-227379400	Weak transcription	NHDF-Ad	bronchial
47	chr1:227370600-227380000	Weak transcription	Gastric	stomach
48	chr1:227370800-227377800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:227370800-227378200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:227371400-227378600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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